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Computational Ecology and Software
Number of Followers: 9  Open Access journalISSN (Print) 2220-721X Published by International Academy of Ecology and Environmental Sciences  [4 journals]
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- Geophysical investigation of Ankashasha dam site, Southern Ethiopia
Authors: Gebre Gidey Weldeabzgi; Mulugeta Markos Tediso.Computational Ecology Software,2023,13(2:27-42
Abstract: The study area, Ankashasha dam site is found in South Nations, Nationalities and Peoples Regional state of Ethiopia. The overall objective of geophysical investigations in the study area is to assist geological studies to determine the depth of bedrock and estimate the probable seepage that might encounter dam reservoir areas. Vertical Electrical Sounding (VES) and two-dimensional electrical resistivity imaging survey methods were used to assess the safety of the Ankashasha dam. The data were acquired from four VES points using Schlumberger cathode arrays with supreme half current electrode spacing, and two-dimensional electrical resistivity imaging three profile data points were analyzed qualitatively and quantitatively to understand the geology and identify aquifer bearing horizons. The qualitative analysis of VES data was accomplished by using curves, apparent resistivity, pseudo-depths, and the quantitative interpretations of the VES data were constructed by the VES data using IpI-res3, IPI2win and Surfer software and constructing geo-electric section sideways profiles using the result from VES point interpretations and lithological information from the Bedesa borehole. The VES results of the data revealed three geoelectric layers that differ in degree of fracturing, weathering and formation. The bedrock is closer to the surface on the delineated fracture boundaries on the geo-electric section of the NE flanks of the axis. The overburden materials consist of seepage flow paths that widen northeastwards parallel to clay, sandy clay and clayey sand. Seismic refraction work should be forwarded since the area is seismically active to map the structures and determine parameters such as densities of eachlayer, weak zones, depth to contacts and others.
- A comprehensive risk assessment system for probabilistic problems
Authors: WenJun Zhang; YanHong Qi, Xin Li.Computational Ecology Software,2023,13(2:43-51
Abstract: In present study we provided a comprehensive risk assessment system. The system consists of four representative methods, namely probability-deterministic assessment, probability-interval assessment, probability-ranking assessment, and probability-ranking with optimal mix strategy. Among them, the probability-interval assessment was proposed by us. In the risk assessment, there are multiple available states, but only one of them can occur in nature. The occurrence probability of each state is the determined value and interval respectively for the first two methods; and for the latter two methods it is the probability difference of each pair of adjacent states. Known the benefit matrix, plans ranking can be derived from the first three methods according to the expected benefit; the fourth method can be used to obtain the optimal mix proportion of plans. The Matlab full code of the assessment system was given for further application and improvement.
- Predicting the shoreline changes in Vishakhapatnam coastal zone using
Multi-output Adaptive Neuro Fuzzy Inference System
Authors: P. Sangeetha; M. Shanmugapriya.Computational Ecology Software,2023,13(1:1-19
Abstract: Coastal erosion is a persistent problem occurring along the Shoreline of India. Several factors that influence the severity of erosion are community infrastructures along the coast, natural disasters, and several man-made activities. There is an increased demand for computing precise information regarding past and present trends and rates of changes in the shoreline. This research investigates the shoreline changes of the Vishakhapatnam district in Andhra Pradesh Coast, as well as finds the quantity of the erosion and accretion rate. Vishakhapatnam having a coastal length of 135 km used for the study, length of study area categorized by fours zones based on the district boundary Zone 1 - Bheemunipatnam, Zone 2 - Vishakhapatnam, Zone 3 - Anakapalli, and Zone 4 - Yellamanchili. The changes in Shoreline were computed with the help of multitemporal satellite images (Landsat 7 and Landsat 4 and 5) for the past 45 years' period, i.e., from 1974 to 2020 using Digital Shoreline Analysis System (DSAS). The rate of shoreline change was accessed using Net Shoreline Movement (NSM), Shoreline Change Envelope (SCE), End Point Rate (EPR), and Linear Regression Rate (LRR). Based on the findings the coastal maps are prepared to estimate the geological changes and shifting of shoreline position. This detailed study is found useful for exploring erosion and accretion processes in the region. About 135 km of coastline was found to be accreting in nature with an average rate of 1.13 m/yr followed by erosion of the shoreline - 0.15 m/yr. The highest and lowest SCE of about 63.4 m/yr and 75.25 m/yr were recorded in Vishakhapatnam Coast. In addition, the Multi-output Adaptive Neuro Fuzzy Inference System (MANFIS) technique is used to predict EPR, NSM, SCE, and LRR for monitoring the shoreline changes, and it could be used for further planning and development and also for disaster management authority in the decision-making process in the study area.
- Mathematical methodology and MATLAB computer program to calculate the
effective-dose of percent response using the probit analysis technique
Authors: M. Tlas; B. A. Ghani.Computational Ecology Software,2023,13(1:20-26
Abstract: Using the probit analysis technique, mathematical algorithm and MATLAB computer program have been implemented in this paper to calculate both the Log-Dose (LD) and the Effective-Dose (ED) for any given percent. The probit analysis uses a successive weighted simple linear regression of experimental or row data. The kind of row data obtained from the bioassays should be generally in percent response (mortality oraffected) at the corresponding doses (or concentrations). The response should be always in binomial form (e.g. death/no death) and the relationship between the response and the various doses or concentrations is always sigmoid or non-linear. The probit analysis here acts as a transformation from sigmoid or non-linear relationship to linear one and then uses a successive weighted simple linear regression on the linearrelationship of the observed data. It is necessarily to note that, the probit analysis always assumes that the relationship between number responding (not proportion response) and dose (or concentration) should be normally distributed. Two simple examples are explained in this paper to prove the validity and the consistency of both the proposed mathematical methodology and the concerning computer program.
- Dilemma of t-tests: Retaining or discarding choice and solutions
Authors: WenJun Zhang.Computational Ecology; Software,2022,12(4:181-194
Abstract: The t-test theory has laid the foundation of modern statistics and it is one of the main contents of statistics. This theory can be found in all statistics textbooks and is at the core of almost all applied statistics courses. At the same time, almost all statistical software or tools have t-test content, such as Matlab, SAS, SPSS, R, etc. However, t-test theory has been widely criticized in recent years due to its theoretical flaws and misuse. The t-test is only used for the problems of normal distribution population with small sample size. Even so, its sample size cannot be too small due to problems such as t-transformation distortion. In terms of significance test, the t-test has the general defects of statistical significance tests, coupled with the inherent fallacies of confidence intervals, and the peculiar uncertainty problems of t-intervals, make the t-test methodology obviously insufficient. The t-test theory is faced with the retaining or discarding decision in statistics, and some statisticians have advocated and abolished the t-test theory from statistics textbooks. As a statistical significance test, the solutions of t-tests include using Bayesian methods, performing meta-analyses, using effect sizes, stressing statistical validity, using nonparametric statistics, using good experimental and sampling designs and determining appropriate sample size, the network methods are used instead of the reductionist method to obtain and analyze the data, and the statistical conclusions are combined with the mechanism analysis to draw scientific inferences, etc. As a t-interval uncertainty problem, its solutions include using the Bayesian credible interval method, using the Bootstrap credible interval method, inferring directly from the central limit theorem, using the unified theory of uncertainty, etc.
- Comparative study and prediction of ambient air quality of Durgapur
Industrial Belt, West Bengal using time series forecast model
Authors: S. Sarkar; S. Sanyal, M. Chakrabarty.Computational Ecology Software,2022,12(4:195-213
Abstract: Time series predictive forecast models can be used to monitor air levels and study, trends in ambient air quality. In this study, we have collected the data of Oxides of Sulphur (SOx), Suspended Particulate Matter (SPM10), and Oxides of Nitrogen (NOx) in Bidhannagar, Durgapur Industrial Belt, West Bengal from the West Bengal Pollution Control Board (2007-2019). The data was analysed both season-wise and month-wise to nullify the irregularity of the data obtained.Time series model can be established only using regular data. The study mainly focused on the comparision between month-wise and season-wise models, in order to identifya prediction model that provides best predictions. The forecast was performed using the seasonal autoregressive integrated moving average (SARIMA) model. The results confirmed that among all forecast models of SARIMA (P, D, Q) (p, d, q) the season-wise model provide best predictions. Graphs indicated a higher concentration of SPM10 and NOx in the winter. The season-wise model for SPM10 (1,0,0)(0,1,1) showed significant higher trends but similar season-wise forecast model for NOx (1,0,0)(0,1,1) showed a decreasing trend. The levels of SPM10 is predicted to show an increasing trend in next four years whereas NOx level is predicted to remain low for the next four years. The seasonal prediction models can be used in understanding the trend in ambient air quality in Durgapur Industrial Belt and facilitate in taking necessary steps to combat the prevailing environmental conditions.
- p-value based statistical significance tests: Concepts, misuses,
critiques, solutions and beyond
Authors: WenJun Zhang.Computational Ecology; Software,2022,12(3:80-122
Abstract: The p-value is at the heart of statistical significance tests, a very important issue related to the role of statistical inference in advancing scientific discovery. Over the past few decades, p-value based statistical significance tests have been widely used in most statistics-related research papers, textbooks, and all statistical software around the world. Numerous scientists in various disciplines hold the p-value as the gold standard for statistical significance. However, in recent years, the p-value based statistical significance tests have been questioned unprecedentedly, mainly because the paradigm of significance tests is wrong, p-value is too sensitive, p-value is a dichotomous subjective index, and statistical significance is related to sample size, etc. Scientific research can only be falsified, not confirmed. p-value based statistical significance tests are one of the sources of false conclusions and research reproducibility crisis. For this reason, many statisticians advocate to abandon p-value based statistical significance tests and replace them with effect size, Bayesian methods, meta-analysis, etc. Scientific inference that combines statistical testing and multiple types of evidence is the basis for producing reliable conclusions. Reliable scientific inference requires appropriate experimental design, sampling design, and sample size; it also requires full control of the research process. For complex and time-varying problems, the network or systematic methods should be used instead of the reductionist methods to obtain and analyze data. To change the scientific research paradigm, the paradigm of multiple repeated experiments and multi-sample testing should be adopted, and multiple parties should verify each other to improve the authenticity and reproducibility of the results. In addition to writing, publishing and adopting new statistical monographs and textbooks, the most urgent task is to revise and distribute various statistical software in the new versions based on the new statistics for further use. Before the popularization of new statistics, what we can do is to improve data quality, strict p-value levels of statistical significance tests, use more reasonable analysis methods or testing standards, and combine statistical analysis and mechanism analysis, etc.
- Foliage biomass of the genera Picea spp. and Quercus spp. in winter
temperature and annual precipitation gradients: Inter-genera paradox in
the forests of Eurasia
Authors: V. A. Usoltsev; H. Lin, S.O. R. Shobairi, I. S. Tsepordey, Z. Ye.Computational Ecology Software,2022,12(3:123-140
Abstract: Current climate change make it increasingly important to assess the response of forest cover biomass to this change, which in turn determines the possibility of climate stabilization by reducing atmospheric CO2. Climate change projections can been linked to significant changes in water deficits and natural disturbance regimes in forest ecosystems across many parts of the world.Since the carbon-deposing potential of a plant community is determined by the biomass of assimilating organs, we focused in this article on comparative analysis of foliage biomass in the dark-coniferous genus Picea spp. and of leaved genus Quercus spp. in gradients of annual precipitation and winter temperature on the territory of Eurasia. The database for modelling involves 870 and 570 sample plots for spruce and oak correspondingly. When studying changes in the biomass of spruce and oak foliage in the hydrothermal gradients of Eurasia, we obtained statistically reliable, but surprising and paradoxical results. When the temperature increases by 1oC, the most increase in spruce foliage biomass occurs in cold regions with insufficient moisture supply, while oak leaf biomass, on the contrary, has the largest percentage of its decrease. In cold regions, as the transition from dry conditions to wet ones, the percentage of foliage mass in spruce decreases, and in oak increases. When the precipitation increases by 100 mm, there is the opposite patterns for spruce and oak: in warm regions, spruce has a decrease in the percentage of foliage mass, and oak, on the contrary, its increase. In the cold regions, these patterns change to the opposite: the spruce negative percentage changes to positive, and the oak positive percentage changes to negative. This phenomenon seems to be related to the positive ratio of photosynthesis and respiration in the spruce during the winter period when the oak does not have photosynthesis, but only respiration. It seems to be related to the fundamental difference between the winter physiology of evergreen and deciduous species, namely the ability of the former to assimilate atmospheric carbon dioxide and prolong the assimilation process beyond the vegetation period, which is usual for deciduous species. The development of such models for the main forest-forming species of Eurasia allow us to predict changes in the foliage productivity of the forest cover of Eurasia in relation to climate change.
- Estimation of carbon stock using ground inventory and remote sensing
imagery in the case of Tiru-Selam Forest, North-western Ethiopia
Authors: E. Gezahegn Gashu; M. Adamsew Marelign.Computational Ecology Software,2022,12(3:141-153
Abstract: Tiru-Selam forest is degraded due to human interventions. Several scholars have studied the carbon stock of various forests using combinations of ground inventory and remote sensing imagery without checking the correlation between these two carbon stock assessment methods. Thus, the study was conducted to determine the carbon stock of Tiru-Selam forest and the correlation of carbon stock estimated by ground inventory and remote sensing imagery. The ground inventory data was collected through a systematic random sampling technique from 400 m2 of 72 sample plots, while the remote sensing imagery data was collected from the National Aeronautics and Space Administration (https://ladsweb.modaps.eosdis.nasa.gov). The moderate resolution imaging spectra-radiometer data was acquired with respect to the ground sampling date. Descriptive statistics were used to calculate the maximum, minimum, mean, and standard deviation of carbon stock. A linear regression model was used to estimate the correlation between ground inventory and remote sensing imagery for estimation of carbon stock in Tiru-Selam forest. According to the ground inventory, and the remote sensing imagery, the overall mean above-ground and below-ground carbon stock of the study area was estimated to be 224.6582 and 226.56 t/ha, respectively. The carbon stock estimated by ground inventory had a strong correlation with the normalized difference vegetation index (NDVI) (r equals to 0.742, p less than 0.05) and the enhanced vegetation index (EVI) (r equals to 0.69, p less than 0.05). The generated equations such as "Y" or estimated forest carbon stock equals to 302.2862 (EVI) + 239.8785(NDVI) + 24.11446 and Y equals to 301.9871 (EVI) + 237.2546 (NDVI) + 21.4254 have been fitted with vegetation indexes at alpha less than 0.05.
- An expert system approach to green stormwater infrastructure selection for
urban area
Authors: L. Ooshaksaraie.Computational Ecology; Software,2022,12(3:154-166
Abstract: The green stormwater infrastructure for urban area is an important, complicate and time-consuming task that relates to huge amount of information, data, domain law, expert knowledge and experience in terms of environmental protection. An expert system has been successfully applied in environmental studies. This paper presents an expert system "ES-GSI" developed by using Microsoft Visual Basic that is used to manage urban area stormwater. To acquire expert experience and knowledge, decision trees and tables are used. For measuring the expert opinion about system rules, certainty factor is used. By using Expert Choice software, multiple experts' opinion is integrated where various alternatives are available. Forward chaining inference mechanism is utilized for results assessment. The proposed ES-GSI are tested and evaluated during all stages of system development for its performance accuracy. System recommendation is displayed in report form. By ES-GSI application, having more accurate decisions will be its benefit.
- Carbon stock variation along environmental gradient of Wacho Forest,
South-Western Ethiopia
Authors: Gezahegn Gashu; Gebre Gidey, Zame Fekansa.Computational Ecology Software,2022,12(3:167-180
Abstract: The carbon stock of forest is disturbed by environmental variables. Therefore, the study was undertaken to examine the variation of carbon sock along environmental gradient of wacho forest, South-Western Ethiopia. A systematic random sampling technique was employed to collect the data from 20 m by 20 m of 73 sample quadrants. Trees and shrubs having not less than 5 cm diameter at breast height were collected from 20 m by 20 m, whereas litter and soil samples were collected from each of the five 1 m by 1 m subplots situated at the four corners and one at the midpoint of the main plot. The carbon stock of trees, shrubs, litter, and soil was determined by using different equations. One-way analysis of variance was used to analyze the variation of carbon stock along environmental gradient of wacho forest, while descriptive statistics were used to estimate the maximum, minimum, mean and standard deviations of carbon stock in the study forest. An altitudinal gradient had a statistically significant effect on dead tree and dead wood carbon, litter carbon, and soil organic carbon. The carbon pools of above-ground carbon, below-ground carbon, dead tree and dead wood carbon, and soil organic carbon were statistically varied with slope gradient. Aspect had a statistically significant effect on the above-ground and below-ground carbon stocks, dead tree and dead wood carbon, litter, and soil organic carbon stock.
- Impact of carbon dioxide emissions caused by human activities on
atmospheric temperature: A mathematical model
Authors: Shyam Sundar; Ashish Kumar Mishra, Ram Naresh, J. B. Shukla.Computational Ecology Software,2022,12(2:23-37
Abstract: Various human activities have increased the concentration of carbon dioxide in the atmosphere leading to increase in average atmospheric temperature causing global warming. It threatens our environment as well as health and basic needs of human beings. Therefore, in this paper, a mathematical model is developed to study the effects of carbon dioxide emissions caused by human activities on average atmospheric temperature contributing global warming considering four dependent variables namely, the density of human population, cumulative density of human activities such as industries, automobiles, and power plants etc., the concentration of carbon dioxide and the average atmospheric temperature. The model is analyzed using stability theory of ordinary differential equations. Local and global stability conditions are established to study the feasibility of the model system. The growth rate of average atmospheric temperature is assumed to be proportional to the increased level of carbon dioxide concentration in the atmosphere from its equilibrium value. It is also assumed that this temperature decreases with a rate proportional to its enhanced level from its equilibrium value caused by various natural factors such as rain fall, snow fall, etc. The analysis shows that as the emission of carbon dioxide from human activities increases the average atmospheric temperature increases considerably from its equilibrium level.
- Estimation of hydraulic parameters using VES sounding and fuzzy techniques
in semi arid Khanasser Region, Syria
Authors: J. Asfahani; Z. Ahmad.Computational Ecology Software,2022,12(2:38-53
Abstract: An alternative approach was developed for evaluating the hydraulic conductivity (K) and the transmissivity (T) of an aquifer. The vertical electrical sounding (VES) measurements and fuzzy techniques (Takagi-Sugeno fuzzy model) are the base of this approach. This approach requires the VES measurements in some points, where available water samples exist to tune fuzzy system with fitting capability, to evaluate the hydraulic parameters. The tuned fuzzy system was used thereafter to extrapolate those parameters, even in VES points where no water samples are available. The Khanasser valley, Northern Syria was taken as a case study to apply the proposed approach. The comparison between the hydraulic parameters values obtained by the proposed approach and those of real pumping test shows an acceptable agreement between them, that attests to the viability of the new proposed technique for characterizing the hydraulic parameters of the aquifers in similar arid and semi arid regions.
- The impact of media coverage on the dynamics of vector-borne diseases
Authors: Aadil Hamid; Poonam Sinha.Computational Ecology Software,2022,12(2:54-66
Abstract: In this paper, the impact of media coverage on the transmission of vector borne diseases has been investigated. The model exhibits two equilibria: a disease-free and a unique endemic equilibrium. The model is analyzed using Hurwitz criterion and Geometric approach. The numerical simulations of model reveals that, the effects of media coverage on the transmission of vector-borne disease endemic may decrease the peak value of the infectives or the average number of the infectives in different cases.
- Estimating and mapping woodland biomass and carbon using Landsat 8
vegetation index: A case study in Dirmaga Watershed, Ethiopia
Authors: M. Adamsew Marelign; D. Temesgen Mekonen.Computational Ecology Software,2022,12(2:67-79
Abstract: This study was conducted to estimate the above and below ground carbon storage in the Woodlands of Dirmaga Watershed, North Western Ethiopia. The field data were collected through systematic random sampling techniques of 40 sample plots. The above-ground biomass and below-ground biomass of the study area was collected from 20 m by 20 m area of the main plot. The biomass and carbon stock of the woodland was estimated using site-specific allometric models and Landsat 8 NDVI and analyzed by ArcGIS. The result showed that the mean carbon stock of above-ground carbon and below-ground carbon were accounted for about 291.47 t/ha and 24.81 t/ha, respectively. The relationship between AGC and NDVI was strong with correlation coefficient of 0.86 and R2 value of 0.745. Tree species of Anogeissus leiocarrpa, Adansonia digitata and Diospyros mespiliformis sequestered the largest portion of the carbon stockwhile, Ficus sycomorus L., Rhus glutinosa and Securinega virosa were the least contributor of carbon stock. The woodland has a great potential for carbon sequestration and biodiversity conservation and the concerned body should conserve and manage the resource properly.
- A geometric morphometric study in the population of Sharpnose Hammer
Coacker (Johnius borneensis, Blecker 1851) from Butuan Bay, Caraga,
Philippines
Authors: C.C. Cabuga Jr.; M. K. A. Angco, Y. G. Codaste, S. M. N. Salvaleon, J. M. D. Pondang.Computational Ecology Software,2022,12(1:1-11
Abstract: Geometric morphometric is an efficient and systematic tool to identify unnoticeable shape differences among biological entities. Sharpnose Hammer Coaker (Johnius borneensis) is a brackish fish and serves as a resource commodity in the study area. The study aims to investigate the body shape variations among its population. 100 individuals comprising 50 males and 50 females of the same size were collected and subjected to Symmetry and Asymmetry Geometric Data Software (SAGE). Procrustes ANOVA shows that males have a significant difference (P less than 0.0001) among the factors analyzed (Individuals, Sides, and Individuals x sides). While females two factors (Sides and Individuals x Sides) show a significant difference (P less than 0.0001), however, the individuals show non-significant. Principal Component Analysis in male fish shows a total of (82.92%) while female shows (84.55%). This implied body shape variation from the collected samples. Thus, it represents a difference in morphology. While indicating a subtle detail on how male populations differ from female populations and vice versa. The importance of geometric morphometric analysis provides a vital tool to define discreet morphological variations among species of the same taxa.
- Susceptible-Infected-Treatment model with disease infection in prey
population recovered by treatment
Authors: S.Saranya; S.Vijaya, E. Rekha.Computational Ecology Software,2022,12(1:12-22
Abstract: This paper describes a mathematical model with Susceptible-Infected-Treatment under disease infection in prey population. The controls methods are one is separating control that is to separate the prey from infected prey by means of self quarantine and the another one as a treatment control that is to reduce the rate of death caused by the disease. A local study of the model is performed around the disease-free equilibrium and the endemic equilibrium to estimate the effect of parameters that control disease spread and species coexistence. Some numerical solutions are given to explain most of the analytical results.
- Causality inference of nominal variables: A statistical simulation
method
Authors: WenJun Zhang.Computational Ecology; Software,2021,11(4:142-153
Abstract: In present study I proposed a statistical simulation method for causality inference of nominal variables (i.e., categorical variables). A new correlation measure for nominal variables, association coefficient, is firstly proposed also. A statistical simulation method was developed to generate artificial data of nominal variables with known causality. The law was then drawn from the simulation analysis of the artificial data. For a set of data of two nominal variables, the randomization method was first used to test the statistical significance of the nominal correlation measure, and then the statistical simulation was used to determine the causality and its statistic significance of two nominal variables. Full Matlab codes of the method were presented.
- Causality inference of linearly correlated variables: The statistical
simulation and regression method
Authors: WenJun Zhang.Computational Ecology; Software,2021,11(4:154-161
Abstract: Causality inference of variables is a research focus in science. Due to its importance, a statistical simulation and regression method for causality inference of linearly correlated (scale or interval) variables was proposed in present study. First, a statistical simulation and regression method was developed to generate and analyze artificial data of linear correlated variables with known causality. The rule was drawn from the simulation and regression analysis on artificial data. Finally, causality inference of two linearly correlated variables was conducted based on the rule. Full Matlab codes of the method were presented.
- Modeling and analysis of the effects of gaseous pollutants and particulate
matters on human health with control mechanisms
Authors: Shyam Sundar; Niranjan Swaroop, Ram Naresh, J. B. Shukla.Computational Ecology Software,2021,11(3:100-125
Abstract: Human health is affected by various types of gaseous pollutants (CO, SO2, NOx, etc.) and particulate matters (PM2.5, PM5, PM10) discharged from several sources such as vehicular traffic, small scale production and construction industries etc. in a city. These particulate matters are also discharged into atmosphere of the city by household emissions, causing respiratory diseases and innumerable deaths of the people. Therefore, in this paper, a nonlinear mathematical model is proposed and analyzed to study the effects of gaseous pollutants and particulate matters on human health in a city with control mechanisms. In the modeling process, six dependent variables are considered, namely, the density of human population, the cumulative density of various pollution emitting sources, the cumulative concentration of gaseous pollutants, the cumulative concentration of particulate matters, the cumulative concentration of suitable aerosols sprayed in the atmosphere to neutralize gaseous pollutants and the number density of water drops (amount of water) to wash out particulate matters from the atmosphere. In the modeling process, it is assumed that the human population density is governed by a logistic model, the growth rate of which decreases due to increased cumulative concentration of gaseous pollutants and particulate matters. It is further assumed that the growth rate of cumulative density of various sources discharging pollutants in the atmosphere is proportional to human population density. The cumulative concentration of aerosol sprayed in the atmosphere is considered to be proportional to the cumulative concentration of gaseous pollutants. Similarly the number density of water drops is assumed to be proportional to the cumulative concentration of particulate matters in the atmosphere. The model is proposed in the form of nonlinear ordinary differential equations which are analyzed by using the stability theory. The model analysis shows that in the absence of any control mechanism, the equilibrium level of population density is lower than that when the control mechanisms are applied. The numerical simulation of the model confirms the analytical findings. This study implies that human health is adversely affected without the control mechanism and the death rate of population increases due to various pollutants emitting sources such as vehicular traffic.
- Interactive statistical computer program for multiple non-linear curves
fitting using stochastic algorithms
Authors: Muhammad Tlas; Bashar Abdul Ghani, Jamal Asfahani.Computational Ecology Software,2021,11(3:126-141
Abstract: An interactive computer program for multiple nonlinear curves fitting has been developed in this work. Several optimization algorithms have been implemented in this software for solving constrained and unconstrained nonlinear optimization models in order to evaluate and best-estimate the concerning and desired suggested mathematical model parameters. Two categories of algorithms have been used in this work. The first category is random and stochastic mathematical methods (nondeterministic methods) such as the simulated annealing and the adaptive simulated annealing. The second category is the direct search methods (deterministic methods) such as Hook-Jeeves pattern search, Fletcher and Reeves conjugate gradient and steepest descent method.
- Stability analysis of a mathematical model for the abatement of methane:
Effect of mitigation options
Authors: Ashish Kumar Mishra; Shyam Sundar, Ram Naresh, J. B. Shukla.Computational Ecology Software,2021,11(2:54-68
Abstract: Atmospheric methane is one of the main greenhouse gases which contribute significantly to increase the burden of global warming. The production of rice paddies and livestock farming are the major sources of methane emissions in the atmosphere. The control of methane emissions using some efficient mitigation options is crucial to lower the concentration of methane in the atmosphere so that the adverse effects of global warming can be reduced to some extent. In this paper, a nonlinear mathematical model is proposed to study the effects of mitigation options on abatement of methane discharged by rice paddies and livestock populations in the atmosphere. In the modeling process, four nonlinearly interacting variables namely, the cumulative density of rice paddies, the cumulative density of livestock populations, the atmospheric concentration of methane and the cumulative density of mitigation options are considered. The cumulative density of mitigation options is assumed to be proportional to the increased level of atmospheric methane concentration from its equilibrium. The proposed nonlinear model is analyzed using the stability theory of differential equations and computer simulations. The study shows that without implementation of mitigation options, the concentration of methane in the atmosphere increases continuously with increase in the rates of its emissions by rice paddies and livestock populations. This increase in the atmospheric methane can be reduced considerably by efficient management of mitigation options. The increase in the implementation rate coefficient of various mitigation options and depletion rate coefficient due to net effectiveness of mitigation options further reduces the atmospheric methane concentration. The numerical simulation of the model confirms the analytical findings.
- Time lag analysis of novel arithmetic modeling in breast cancer
Authors: Kalyan Das; Ranjith Kumar, Pankaj Taneja, M Lutfor Rahman.Computational Ecology Software,2021,11(2:69-82
Abstract: In this paper, a mathematical model which considers population dynamics among infected and uninfected cancer tumor cells has been proposed. Delay differential equations have been utilized to demonstrate the framework to consider the periods of the cell cycle. We examine the steadiness of the framework and demonstrate a hypothesis dependent on the contention standard to decide the dependability of a fixed point and show that the solidness may rely upon the delay. We show hypothetically as well as through numerical results that periodic oscillations may arise through Hopf bifurcations. In this paper we study a stochastic model for the conduct of malignancy tumors, depicted by a stochastic differential condition with multiplicative noise term. We study the existence of the solution process, as well as its behavior in the framework of stochastic inclusion problems and long time behavior.
- Impact of human activities on forest resources and wildlife population
Authors: Rachana Pathak; Vinay Verma, Manju Agarwal.Computational Ecology Software,2021,11(2:83-99
Abstract: Nowadays, management and regulation of natural resources like agriculture, fisheries, forestry and wildlife is one of the popular topics in research. The evolution of humankind is largely dependent on the quality of the environment and the resources it provides; but numerous human-induced factors, and climate change may drastically change the conditions of human sustainability. A wide range of human activities on forestland contribute to climatic change, prominent among these are, deforestation, desertification, industrialization, urbanization and other socio-economic activities. In this paper, attempts have been made to trace the causes and consequences of these human activities on the depletion of forestry resources. A nonlinear mathematical model is proposed and analyzed. In modeling process, we assume that the growth rate of wildlife population wholly depend on forestry biomass. It is depleted by human activities. Local and global stability analysis of the mathematical model along with the persistence of the system is checked using theory of nonlinear ordinary differential equations. Analytical results obtained are justified numerically through numerical simulation. Important parameters are investigated and variation of variables with change in these parameters is determined.
- Analysis of a model for carrier dependent infectious diseases with
sanitation as a control strategy
Authors: Ram Naresh; Sandhya Rani Verma, J. B. Shukla, Manju Agarwal.Computational Ecology Software,2021,11(1:1-20
Abstract: The sanitation plays a very important role to control the spread of infectious diseases and is much effective public health intervention. Inadequate sanitation is a major cause of spread of carrier dependent infectious diseases such as typhoid, dysentery and cholera. In this paper, a nonlinear mathematical model is proposed to study the effect of sanitation on the spread of such diseases in a homogeneously mixed human population. In modeling the process, it is assumed that the disease spreads directly from the infectives to susceptibles as well as indirectly by the carriers present in the environment. The density of carrier population is assumed to grow logistically but it declines due to sanitation effort applied whereas the sanitation effort also follows a logistic model with its desired increase taken directly proportional to the density of carrier population. The proposed model is also extended to an optimal control problem and is analyzed using Pontryagin Maximum Principle. The model analysis reveals that the carrier population density decreases with increase in the sanitation effort applied resulting to decrease the infective population and hence decline in the disease prevalence. Thus, the spread of carrier dependent infectious diseases can be controlled significantly if suitable sanitation effort is applied to curb the carrier population in the environment. Numerical simulations performed also support the analytical findings.
- Dynamical analysis of discretized Logistic model with Caputo-
Fabrizio
fractional derivative
Authors: H. Karakaya; I. Ozturk, S. Kartal, F. Gurcan.Computational Ecology Software,2021,11(1:21-34
Abstract: In this paper we consider a fractional order Logistic model with Caputo-Fabrizio fractional derivative. By applying two-step Adams-Bashforth scheme, we obtain a system of difference equations. By using the Schur-Cohn criterion, stability conditions of the positive equilibrium point of the discrete system are obtained. It is observed that the discrete system shows much richer dynamic behaviors than its fractional-order form such as Neimark-Sacker bifurcation and chaos. The direction and stability of the Neimark-Sacker bifurcation are determined by using the normal form and center manifold theory. In addition, the effect of fractional order parameter on the dynamical behavior of the system is investigated. Finally, numerical simulations are used to demonstrate the accuracy of analytical results.
- Geometric-morphometric analysis of wing shape of Lucilla sericata Meigen
(Diptera: calliphoridae) from two different environments
Authors: J. R. Pucot; D. M. E. Guadalquiver, C. G. Demayo.Computational Ecology Software,2021,11(1:35-45
Abstract: The common green blowfly, Lucilia sericata, is a widespread species with forensic, medical, and veterinary importance. In this study, we use geometric morphometric as a tool to assess differences in the wing shape of female L. sericata occurring on two different environs. Thirty samples were collected from the two sites of Poblacion Market and Pampam Falls, Iligan City. The right wings were dissected and previously identified landmarks were digitalized using TpsDig. Morphometric analysis was conducted through Generalized Procrustes-based analysis, together with the quantification of wing area and length. Subsequent discriminant analysis was also conducted through PAST software. Results revealed intraspecific variations with greater than 70% statistically significant discrimination. 83.33% of studied individuals were correctly classified into their corresponding group on the first discriminant function. A total of twelve significant components contributed to the differentiation of the female L. sericata right wings from two environs. Amongst the significant components identified, Principal Component 1 contributed the highest to the variation with 20.95% shape variability. Most variability are from the landmarks of the upper margin and middle portion of the wings extending to the branching endpoint of the media vein. The results showing variation within species were accounted as phenotypic plasticity to contrasting environmental conditions.
- Agricultural activities impacts on water resources of Masouleh river basin
with WEAP model
Authors: Rahil Rahimi; Leila Ooshaksaraie, Hasan Karimzadegan.Computational Ecology Software,2021,11(1:46-53
Abstract: The Masouleh river basin is in south of Iran. Different water user such as urban, rural, agriculture and industry are presented in the catchment. Municipal, rural, agricultural, industry and environmental need are going exacerbate future water resources management. The agricultural activities are related to a range of environmental factors such as conservation of the natural resources, water and biodiversity. WEAP capabilities are extensive related to water resources for municipal and agricultural sector including water conservation, ware allocation priorities, water demand and ecosystem requirements. In this study, three scenarios (Reference, Change of priority and Agriculture reuse Scenario) were selected in order to assess the impact of water demands on the water resources of the Masouleh River catchment in 2035. Scenario made in the current situation and the model enabled analyses of unmet water demand for each scenario for 25 years (from 2011 to 2035). The results of the study showed that Change of priority scenarios water supply is not insufficient to completely meet the demands of all sectors therefore, reuse scenario is the next priority. Application of Water Conservation and Demand Management practices and improvement water distribution can reduce the unmet demand.
- Solutions for better fitting Sigmoid-shaped functions to binary data
Authors: V.M.N.C.S. Vieira.Computational Ecology; Software,2020,10(4:162-185
Abstract: Sigmoid-shaped curves are often used to estimate the probability of individuals surviving or becoming fecund (response: y) given some characteristic like age or size (predictor: x). However, the individual observations of y used to calibrate the curve are binary (0 or 1) because each individual either survived or not, and was fecund or not. A Matlab-based software is here demonstrated by fitting Gompertz and Weilbull curves to the probabilities of the red alga Gracilaria chilensis becoming fecund depending on frond size. Different approaches are possible for parameter estimation, namely, minimizing the error sum of squares or maximizing the log-likelihood. Because neither have analytical solution, both were estimated by numerical methods as the Gauss-Newton, the Newton-Raphson, the Levenberg-Marquardt and the Matlab built-in fmincon function. Assuming x is bell-shape distributed, all these alternatives optimize the curve-fit to the bulk of the data i.e., in the middle of the curve. However, in this case the accuracy of the fit in the curve extremes was of utmost importance. A misfit could lead to a 124% change in estimated overall spore production. To balance the weight of curve sections, the observations were grouped into x classes and the curve was fit to their mean y. However, the small sizes of groups in the extremes rouse problems of numerical instability and uncertainty. The Gompertz curves were easier fit and could be done by any method while the Weibull curve could only be well fit by the Newton-Raphson method. Possible measures to improve convergence were the choice of initial guesses, decrease the step-size of the search, use a positive definite matrix re-directing the search or not using classes with too little observations inside.
- The fuzzification of mathematical matrix in the environmental impact
assessment of steel industry, Ghayen, Iran
Authors: J. Dawoudian; Sr. Ahmadizadeh.Computational Ecology Software,2020,10(4:186-199
Abstract: Ghayenat steel complex is located in South Khorasan province near the Nimbolook city. In this research, the interactions between basic and supplementary criteria are evaluated using a mathematical matrix. The results of the meaningful impact are divided into four categories: low, middle, high, and very high. In this research, the effects of synergism and disagreement among experts are used as quantitative factors affecting environmental impacts in matrix calculations. The results of the mathematical matrix are fuzzyficated using a minimal operator in a triangular diagram. By including the compensating factor, the results of the mathematical matrix illustrate that only low and middle classes have impacts on the environment. Also, high and very high classes have a small share in the impact. On the other hand, according to the results, most activities are related to the middle and low classes for the basic criteria. Most of the interactions are associated with the low impacts on the supplementary criteria. Fuzzification shows that if the compensating factor is not applied, the highest impacts will be in the middle and high classes. If the compensating factor is applied, 0.73% of the impacts will be in the middle class, and the very large class has a small share. Also, due to the impacts of the compensatory criteria, the project is approved in both ways.
- Dynamic complexity in a discrete-time predator-prey system with Holling
type I functional response: Gompertz growth of prey population
Authors: Sarker Md. Sohel Rana.Computational Ecology; Software,2020,10(4:200-216
Abstract: We consider a discrete-time predator-prey system with Holling type I functional response and Gompertz growth of prey population to study its dynamic behaviors. We algebraically show that the predator-prey system undergoes a flip bifurcation (FB) and Neimark-Sacker bifurcation (NSB) in the interior of R2+ when one of the model parameter crosses its threshold value. We determine the existence conditions and direction of bifurcations by using the center manifold theorem and bifurcation theorems. We present numerical simulations to illustrate theoretical results which include the bifurcation diagrams, phase portraits, appearing or disappearing closed curves, periodic orbits, and attracting chaotic sets. In order to justify the existence of chaos in the system, maximum Lyapunov exponents (MLEs) and fractal dimension (FD) are computed numerically. Finally, chaotic trajectories have been controlled by applying feedback control method.
- How to calculate statistical power for vegetation research
Authors: Mohammad Mousaei Sanjerehei.Computational Ecology; Software,2020,10(4:217-237
Abstract: Calculation of statistical power is important for proper interpretation of research results. Statistical Power depends on the selected significance level, sample size and effect size. Selection of an appropriate formula for calculating power of a test is dependent on the study design, type and statistical distribution of data and the statistical test. In this paper, several formulas are presented with examples for calculating power for one sample mean test and one sample proportion test, comparing between two independent groups and two paired groups, correlation analysis, simple and multiple linear regression, simple and multiple logistic regression, contingency tables and analysis of variance (ANOVA).
- A generalized discrete dynamic model for human epidemics
Authors: WenJun Zhang; ZeLiang Chen, Yi Lu, ZhongMin Guo, YanHong Qi, GuoLing Wang, JiaHai Lu.Computational Ecology Software,2020,10(3:94-104
Abstract: A discrete dynamic model for human epidemics was developed in present study. The model included major parameters as transmission strength and its dynamic changes, mean incubation period, hospitalization time (i.e., the time from illness to hospitalization), non-hospitalization (i.e., outside hospitals) daily mortality, non-hospitalization daily recovery rate, and hospitalization proportion (proportion of cases for hospitalization), etc. Sensitivity analysis of the model indicated the total cumulative cases significantly increased with the increase of initial transmission strength and hospitalization time. The total cumulative cases significantly decreased with the increase of transmission strength's dynamic decline and hospitalization proportion, and decreased with the increase of non-hospitalization daily mortality and non-hospitalization daily recovery rate. The total cumulative cases significantly increased with the decrease of mean incubation period. Sensitivity analysis demonstrated that dynamic change of transmission strength is one of the most important and controllable factors. In addition, reducing the delay for hospitalization (i.e., hospitalization time) is much effective in weakening disease epidemic. Enhancing immunity to recover from the disease is of importance for increasing non-hospitalization recovery rate.
- Taxonomic identification of hoverfly specimens using neural network and
gradient boosting machine techniques
Authors: Dunja Popovic; Vuk Popovic, Nevena Velickovic, Ante Vujic.Computational Ecology Software,2020,10(3:105-116
Abstract: The correct identification of single specimens on a particular area has great importance in establishing appropriate biodiversity protection programs. Species of the genus Merodon Meigen, 1803 (Diptera, Syrphidae) represent important pollinators that are particularly associated with the pollination of wild and cultivated bulbous plants, both wild and cultivated. In order to contribute to a taxonomic issue of separating two cryptic, sibling hoverfly species of M. avidus species complex, we programmed and trained specific prediction model that was able to specify to which of two assumed species (M. avidus or M. moenium) each database specimen belongs. Using two ML techniques (artificial neural network (ANN) and gradient boosting machine (GBM)), we created two separable models, depending on a variable used for a prediction (Model 1 - modelling based on a geographic variable, Model 2 - modelling based on a temporal variable). Moreover, each model was trained and tested with different data sets, resulting in a different predictive accuracy. While ANN modelling showed a higher percent of correct determination when using surrogate information than when using reduced (basic) data set, GBM modelling has given a quite stable result through all three data types. In both ML approaches, comparing Model 1 and Model 2 results showed that prediction based on a temporal variable (day, month and a year of specimen sampling) reached a better predictive performance than a prediction based on a longitude and latitude, on all data sets. This led us to the conclusion that information about the time of sampling was more useful for creating desired determination key with artificial intelligence algorithms than information about longitude and latitude of sampling localities. Therefore, we suggest that time of activity of adult specimens could have been of greater importance in the differentiation of M. avidus and M. moenium species from a common ancestor. The environmental factors and selective forces connected with the season might have had a more important role in M. avidus / M. moenium speciation, compared to environmental factors / selective pressures connected with the geographic position of their activity. The demonstrated modelling represents a positive signal in the field of potential implementation of these systems as support in the initial determination Merodon specimens. We suggest it2s potential use as technical support in old and partially unreliable databases, in determination of fresh sampled specimens as well as in finding the most efficient sampling strategies.
- Dynamic complexity in a discrete-time predator-prey system with
Michaelis-Menten functional response: Gompertz growth of prey
Authors: Sarker Md. Sohel Rana.Computational Ecology; Software,2020,10(3:117-132
Abstract: A discrete-time predator-prey system with Michaelis-Menten functional response and Gompertz growth of prey is examined to reveal its chaotic dynamics. We prove algebraically that when one of the model parameter passes its critical value, the system passes through a flip bifurcation (FB) and Neimark-Sacker bifurcation (NSB) in the interior of R2+. We apply the center manifold theorem and bifurcation theorems to determine the existence conditions and direction of bifurcations. Numerical simulations are employed which include the diagram of bifurcations, phase portraits, periodic orbits, invariant cycle, abrupt emergence of chaos, and attracting chaotic sets. In addition, maximum Lyapunov exponents (MLEs) and fractal dimension (FD) are computed numerically to justify the existence of chaos in the system. Finally, we apply feedback control method to control chaotic trajectories.
- Interactive software for classification and ranking procedures based on
multi-criteria decision-making algorithms
Authors: M. Tlas; B. Abdul Ghani.Computational Ecology Software,2020,10(3:133-150
Abstract: Interactive software that helps the decision maker to choose the optimal ranking for complex systems has been prepared according to multiple preference criteria. The code algorithm is based on famous mathematical methods well known in multi-criteria decision making, such as VIKOR, TOPSIS, and the weighted sum method (WSUM). This code is used at the AECS to assess and classify the performance of employees or for inter-departmental comparison according to their scientific and technical output performance. It can also be used in wider fields outside the AECS according to preference criteria carefully selected by the decision-maker. Beneficiaries might include Syrian private and state universities or academics. Criteria elements can, for example, be drafted along international standards of copyrighted internal reports, published papers, journal impact factor, journal citations, H-index and registered patents. Two real examples are explained in this paper to prove the validity and consistency of this computer code.
- Stability analysis of a system of second order rational difference
equations
Authors: Muhammad Salman Khan; Qamar Din, Maria Habib, Muhammad Asif Khan.Computational Ecology Software,2020,10(2:44-58
Abstract: In this paper we consider a system of second order rational difference equations. We mainly discuss the boundedness and persistence, existence of fixed point, and uniqueness of positive fixed point, local and global behavior of positive fixed point and rate of convergence of every positive solution of the system under discussion. It will be shown that the system under discussion exhibits some special dynamics such as same mathematical condition for existence of fixed point and its global stability. Finally, some numerical examples are provided for verification of theoretical results.
- Role of environmental factors on the spread of bacterial diseases: A
modeling study
Authors: Sandhya Rani Verma; Ram Naresh, Manju Agarwal, Shyam Sundar.Computational Ecology Software,2020,10(2:59-73
Abstract: In this paper, a nonlinear mathematical model is proposed and analyzed to study the role of cumulative environmental degradation on the spread of bacterial diseases. In the modeling process, it is assumed that the disease is not only transmitted directly from the infective population to susceptible population but also indirectly by the bacteria present in the conducive degraded environment. The cumulative density of the bacteria population is assumed to be governed by a generalized logistic model, and is also dependent on conducive environmental degradation. The cumulative density of environmental degradation is assumed to be dependent on human population-related factors. The analysis of the model is performed by using the stability theory of differential equations and numerical simulation. The model analysis reveals that the increased rate of conducive environmental degradation increases the density of bacteria population which leads to fast spread of the bacterial diseases.
- Understanding of plankton patterns and complex spatial interaction among
nontoxic phytoplankton, toxic phytoplankton and zooplankton populations
Authors: Rashi Gupta.Computational Ecology; Software,2020,10(2:74-93
Abstract: In this paper, I have proposed a mathematical model for aquatic ecosystem with three interacting species, toxin-producing phytoplankton (TPP), non-toxin producing phytoplankton (NTP) and zooplankton with Holling type II functional responses. I have carried out a detail study of stability analysis for the non-spatial and spatial model systems and obtained the conditions for diffusive instability. I have also performed the numerical simulation for a particular set of parameter values which is realistic for natural planktonic system. The numerical results revealed the following: (i) dominant TPP population is under control which is essential for aquatic systems, (ii) cyclic behavior of NTP, TPP and zooplankton population in heterogeneous biomass distribution, and (iii) the evolution of patchy non-Turing patterns. The overall result may be useful for sustainability and maintenance of biodiversity of aquatic systems.
- Modeling the dynamics of methane emission from rice paddies and livestock
populations and its effects on global warming: A comparison of model with
data
Authors: Shyam Sundar; Ashish Kumar Mishra, Ram Naresh, J. B. Shukla.Computational Ecology Software,2020,10(1:1-14
Abstract: The rice paddies and livestock populations are the largest anthropogenic sources of methane emissions in the atmosphere causing global warming. In this paper, a nonlinear mathematical model is proposed and analysed to study the effect of methane emissions on global warming by considering four dependent variables, namely, the cumulative biomass density of rice paddies, the cumulative density of livestock populations, the atmospheric concentration of methane emitted from rice paddies, livestock populations as well as natural sources and the average global warming temperature of near earth's atmosphere. In the modeling process, it is assumed that both the cumulative densities of rice paddies and livestock populations follow logistic models with their respective growth rates and carrying capacities. The livestock populations are assumed to be partially dependent on rice paddies for food. Further, the livestock populations are assumed to be harvested for meat and leather. The growth rate of methane concentration in the atmosphere is assumed to be proportional to the cumulative density of rice paddies as well as of livestock populations. This growth rate also increases with a constant rate from natural sources but it decreases with a rate proportional to its concentration in the atmosphere due to various factors. The growth rate of global warming temperature is assumed to be proportional to the increased level of methane concentration in the atmosphere from its equilibrium value. It is also assumed that this temperature decreases with a rate proportional to its enhanced level from its equilibrium value caused by various natural factors such as rain fall, reforestation, etc. The model is analyzed by using stability theory of ordinary differential equations and computer simulation. The analysis shows that as the emissions of methane from rice paddies and livestock populations increase, the global warming temperature increases considerably from its equilibrium level. The percentage increase in global warming temperature with the corresponding increase in methane concentration is determined from the model and compared with the available data in the literature. The comparison is found to be very satisfactory. The numerical simulation confirms this result.
- Local dynamical properties and supercritical N-S bifurcation of a
discrete-time host-parasitoid model with Allee effect
Authors: A. Q. Khan; M. Askari, H. S. Alayachi, M. S. M. Noorani.Computational Ecology Software,2020,10(1:15-43
Abstract: We explore thelocal dynamical properties and supercritical N-S bifurcation of the following Beddington model with Allee effect in R2+:xt+1=xt exp(r(1-xt)-yt), yt+1=m xt (1-exp(-yt)) yt/(B+yt),where xt (respectively yt) denotes densities of host (respectively parasitoid) at time t, r and m respectively denotes number of eggs laid by host and parasitoid which survive through larvae, pupae, and adult stages, and B is constant. More specifically, we explored that model has three equilibria namely the trivial, boundary and positive equilibrium point. We studied the local dynamics along with topological classification about equilibria of the under consideration model. We also explored the existence of bifurcation about equilibria of the model. It is proved about boundary equilibrium point parasitoidgoes to extinction whilehost population undergoes a flip bifurcation to chaos by taking r as bifurcation parameter. It is explored that aboutpositive equilibrium point, model undergoes N-S bifurcation and in meantime invariant closed curve appears. In the perspective of the biology, these curves correspond to periodic or quasi-periodic oscillations between host and parasitoid populations. Finally theoretical results are verified numerically.
- Experimental and theoretical evaluation of bifacial photovoltaic thermal
collectors
Authors: P. Ooshaksaraei; L. Ooshaksaraie, M. Seyednezhad, M. H. Yazdi, K. Sopian.Computational Ecology Software,2019,9(4:121-133
Abstract: This paper represents the theoretical and experimental performances of solar collector using an array of a single pass - air photovoltaic (PV) cells; replacing a diffuse reflector under a bifacial PV module (with an acceptable distance) instead of conventional absorber plate of photovoltaic-thermal (PVT) collectors. Energy and exergy analysis of the solar collector is done by mathematical modeling in one-dimensional steady state condition (1D-SS). A collector rack was designed and fabricated to examine and verify the theoretical model. The steady state exergy efficiency of 4.2 - 10% and energy efficiency 17 - 62% detected for both 0.04 - 0.13 kg/s and 0.22, 0.33, 0.50 and 0.67 of airflow rate and packing factor respectively. The prevailing output of the collector is thermal energy while electricity is the dominant output of exergy. In the range of 0.04 - 013 kg/s, airflow rate has no influence on the overall exergy of the collectors due to the strong dependency of the total exergy on electrical output rather than thermal one. Finally, as the result of increasing airflow rate, the overall output energy of the collector increases due to the increase of the thermal energy harvest.
- Sexual shape dimorphism in the monomorphic fish Decapterus macrosoma
(Teleostei: Carangidae)
Authors: Kaent Immanuel N. Uba.Computational Ecology; Software,2019,9(4:134-142
Abstract: Monomorphism is prevalent among fishes consequently sexually dimorphic traits are unknown. Discrimination between sexes is often achieved through direct examination of the gonads. However, at present, patterns of sexual dimorphism are known through the analysis of body shapes. Thus, this study used landmarkbased geometric morphometrics to investigate and describe sexual dimorphism in the body shape of Decapterus macrosoma. Fourteen landmarks from images of 60 individuals (25 males and 35 females) were subjected to geometric morphometric analysis. Variability in body shapes between sexes was visualized by generating thine-plate spline expansion plots. Results showed that females exhibited a deeper body depth, broader belly region, bigger head, and wider caudal fin while males exhibited a narrow body depth, smaller head, and wider dorsal and caudal fins. Multivariate analysis of variance and discriminant function analysis showed significant difference in the body shapes between sexes of this fish species (p less than 0.05). The results were discussed as results of sexual and natural selection in fishes.
- Chaotic behavior of harvesting Leslie-Gower predator-prey model
Authors: Muhammad Asif Khan; Muhammad Sajjad Shabbir, Qamar Din, Khalil Ahmad.Computational Ecology Software,2019,9(3:67-88
Abstract: This article deals with the study of some qualitative properties of a harvesting Leslie-Gower predator-prey model. Particularly, we explore the existence, uniqueness, boundedness of positive equilibrium point and local stability analysis of positive equilibrium point. Moreover, it is shown that there exists period-doubling bifurcation and Nimark-sacker bifurcation for the unique positive steady-state of given system. In order to control the bifurcation we introduce a feedback strategy. For further confirmation of complexity and chaotic behavior largest Lyapunov exponents are plotted.
- Dynamics of three species plankton model with Holling type-IV functional
responses and control of toxic phytoplankton
Authors: Rashi Gupta.Computational Ecology; Software,2019,9(3:89-106
Abstract: In this paper we proposed a minimal model of non-toxic phytoplankton - toxic phytoplankton - zooplankton dynamics with Holling type-II and Holling type-IV functional responses. We carried out the analytical study of spatial and non-spatial model for one dimensional system in detail and found out the condition for diffusive instability of a locally stable equilibrium. With the help of numerical simulations, we have observed that when the rate of inhibition of zooplankton growth by toxic material ingested in feeding on toxic phytoplankton is very large, then because of high toxic effect, the zooplankton goes to extinction.
- Sexual dimorphism, asymmetry, and allometry in the shell shape of Modiolus
metcalfei (Hanley, 1843) collected from Dumangas, Iloilo, Philippines: A
geometric morphometric approach
Authors: K.I. N. Uba; H. M. Monteclaro, M. M. P. Noblezada-Payne, G. F. Quinitio.Computational Ecology Software,2019,9(3:107-120
Abstract: The shell is the most conspicuous and variable part of a bivalve and is largely affected by environmental conditions. Thus, this study was conducted to describe the changes in the shell shape of the horse mussel Modiolus metcalfei from Dumangas, Iloilo. Allometric changes in shape, sex-induced shape differences, and asymmetry were investigated using geometric morphometric methods. A total of 12 landmarks where used to obtain biological shape information from 60 horse mussel individuals. Multivariate analysis of variance revealed significant differences of shell shapes between sexes (Wilk's lamda=0.01, p=1.26E-219). Generally, males have an expanded shell but compressed mid-shell region while females have compressed shell but expanded mid- and postero-ventral region. Moreover, the multivariate regression of shape on centroid size was statistically significant (p less than 0.001, Goodall's F-test). Smaller individuals were slender and elongate while larger individuals were slightly rounded and curved.Furthermore, directional and fluctuating asymmetry were highly significant (p less than 0.0001, Procrustes ANOVA), indicating developmental instability probably caused by the ecological health of the coastal waters of Dumangas, Iloilo. The differences in shape between sexes were attributed to the differences in reproductive roles while allometric shell morphology changes reflected its adaptation to the environment.
- Bifurcation analysis and chaos control in a discrete-time predator-prey
system with Crowley-Martin functional response
Authors: S. M. Sohel Rana.Computational Ecology; Software,2019,9(2:37-57
Abstract: In this paper, the dynamics of a discrete-time predator-prey system with Crowley-Martin functional response is examined. Via application of the center manifold theorem and bifurcation theorems, we algebraically show that the system undergoes a bifurcation (flip or Neimark-Sacker) in the interior of R2+. Numerical simulations are presented not only to validate analytical results but also to reveal new dynamical behaviors which include bifurcations, phase portraits, period- 5, 6, 7, 10, 11, 15, 16, 17, 21, 28, and period- 51 orbits, invariant closed cycle, sudden disappearance of chaotic dynamics and abrupt emergence of chaos, and attracting chaotic sets. Furthermore, maximum Lyapunov exponents and fractal dimension are computed numerically to justify the chaotic behaviors of the system. Finally, we apply a strategy of feedback control to control chaos exists in the system.
- Fractal analysis of Hippocampus spp. (seahorse) from Surigao City,
Philippines
Authors: S. R. M. Tabugo; R.C.M. H. Ortega, C. S. Padasas.Computational Ecology Software,2019,9(2:58-66
Abstract: Assessment of species can be promising for ecosystem and environment sustainability. The demand for trading and environmental impact becomes the culprit to decline in seahorse population. Hence, this paved way for the emergency of plausible non-destructive method and tools for monitoring to measure risks and vulnerability. The area near Surigao city, had been popular due to mining practices and also a famous route for seahorse trade in Mindanao. The aim of this study is to use fractal geometry to look into morphometric complexity patterns of different species of seahorses (Hippocampus spp.) in Surigao City. Irregular non-Euclidean objects are better described by fractal geometry and the measurable value is called the fractal dimension. Box-counting and lacunarity method were performed with FracLac v.2.5, and available as a plugin to ImageJ. The method was done to test whether significant differences in fractal dimension and lacunarity values can be speciesspecific and provide evidence of vulnerability. It is hypothesized that fractals are far from the equilibrium state and thus associated with chaos. Thus, high fractal dimensions have implications to vulnerability of species. High fractal dimension based on box-counting and lacunarity method was associated with H. comes. The results for fractal dimensions (DB) were in accordance with the coefficient of variation (CV) values. Information obtained aide in understanding the nature of species in Surigao city.
- Three different ways for estimating Green Oak Leaf Roller dynamics type:
OLS, MEP, and Almost-Bayesian approaches
Authors: L.V. Nedorezov.Computational Ecology; Software,2019,9(1:1-18
Abstract: The generalized discrete logistic model (GDLM) of population dynamics was used for fitting of the known empirical time series on the green oak leaf roller (Tortrix viridana L.) fluctuations in European part of Russian Federation (Korzukhin and Semevsky, 1992). The model was assumed to demonstrate satisfactory data approximation if and only if the set of deviations of the model and empirical data satisfied several statistical criterions (for fixed significance levels). Distributions of deviations between theoretical (model) trajectories and empirical datasets were tested for symmetry (with respect to the ordinate line by Kolmogorov-Smirnov, Mann - Whitney U-test, Lehmann - Rosenblatt, and Wald - Wolfowitz tests) and the presence or absence of serial correlation (the Swed-Eisenhart and ''jumps up-jumps down'' tests). Stochastic search in a space of model parameters show that the feasible set (set of points where all used tests demonstrate correct/required results) is not empty and, consequently, the model is suitable for fitting of empirical data. It is also allowed concluding that observed regime of population dynamics isn't cyclic (if length of cycle is less than 1500 years) and can be characterized by the fast decreasing autocorrelation function (with further small fluctuations near zero level). Feasible set allows constructing almost-Bayesian estimations of GDLM parameters. For the situation when model parameters are stochastic variables algorithm of calculation of model trajectories is presented.
- Crowding effects and depletion mechanisms for population regulation in
prey-predator intraspecific competition model
Authors: Kumar G. Ranjith; Das Kalyan, K. Lakshminarayan, Reddy B. Ravindra.Computational Ecology Software,2019,9(1:19-36
Abstract: The current investigation centres on the consequences of intra-specific rivalry involving predators in the predator-prey equation. A careful account of the investigation is offered mathematically of the model to offer insights into important outcomes that result from the interplay of deterministic and stochastic process. In particular, the steadiness and bifurcation investigation of this model find mention. Allowance is also made in this model for a stochastic environment impacted by white noise. While for this particular version, the global stability is predicated under conditions bordering on stochasticity close to environmental concerns. Rivalry among the predator population is without a doubt accommodating for a various predator-prey models by keeping population stable at a positive interior equilibrium. Numerical solutions obtained for the models support the assumptions governing the study.
- Sexual dimorphism in the carapace of mud crab (Scylla serrate, Forsskal,
1775) in Magallanes, Agusandel Norte using Geometric Morphometric Analysis
Authors: C. J. Presilda; M.A. Salcedo, M. J. Moreno, J. Cogenera, R.A. Japitana, J. H. Jumawan, J. C. Jumawan, J. Presilda, C.J.R. Presilda, E.A. Requieron, M.A.J. Torres.Computational Ecology Software,2018,8(4:88-97
Abstract: The study was conducted mainly to describe and analyse the sexual dimorphism using carapace shape in both sexes of S. serrata collected from Magallanes, Agusandel Norte using geometric morphometrics as a tool. On the other hand, Landmark-based methods utilize biological equivalences on the homologous structures of an organism. It aims to note the position of important landmarks, amputating irrelevant data as to differences in size, rotation, and locations of the biomarker using Thin Plate Splice (TPS). This method was employed to discriminate differences between male and female and to describe various variations that occur in the form of biomarkers in response to its situations. A total of 60 individuals (30 males and 30 females) were subjected to relative warp analysis. Land-mark analysis was obtained using TPS series with 33 landmarks generated for each samples and loaded into tpsrelww32 to assess the distinction in the body shape between male and female S. serrata. Sexual dimorphism of S. serrata from Magallanes, Agusan del Norte can be seen between the two sexes, based on the MANOVA test that results to a relative significant difference that is presented and further visualized in the Canonical Variation Analysis (CVA) that produces scatter plot along the two canonical axes (X and Y axes), producing a separation of the two sexes.
- Relative warp analysis of wing shape variations in three selected
populations of Aedes aegypti Linnaeus
Authors: Danilo A. Gualberto; Cesar G. Demayo.Computational Ecology Software,2018,8(4:98-111
Abstract: Population variations in the dengue vector mosquito, Aedes aegypti (Linneaus) was examined using landmark based Geometric Morphometric methods of the left and right wings for both sexes from among three locations in the city of Cagayan de Oro, Philippines. Relative Warp Analysis (RWA) was conducted on both wings based on shape scores for the detection of variations within and between the three populations. Canonical variate analysis (CVA) of the relative warp scores yielded Wilk's lambda that were very near zero and Pillai trace that were at or near values of 1 indicating that wing shape scores among the three populations of mosquito had means that were different from each other. Discriminant analysis have shown the three Aedes aegypti populations differ significantly (greater than 70% correct classification) based on the male's left and right wings and the females' right wing. The rural population was also correctly classified based on the right wings of both sexes. What is interesting in the results is that all three populations were not correctly classified based on the female's left wing. These indicate that the wings of the rural male and all the female populations of Aedes aegypti were asymmetrical in shapes which may be due to genetic, developmental, or as a result of environmental processes and are "probably normally adaptive". These findings strongly demonstrate strong infraspecific variations in wing structures of Aedes aegypti at different areas of Cagayan de Oro City.
- Geometric morphometrics of leaf blade shape in water hyacinth (Eichhornia
crassipes: Pontederiaceae) population from Lake Mainit, Philippines
Authors: C.C. Cabuga; Jr, I.C.B. Delabahan, J.I.C. Dedel, M.A. Ayaton, L.A. Ombat, M.L.M. Budlayan.Computational Ecology Software,2018,8(2:46-56
Abstract: This study was carried out in order to investigate the leaf blade shape variation in the populations of water hyacinth (Eichhornia crassipes) from Lake Mainit, Philippines using geometric morphometric analysis. A total of 120 leaf individuals were randomly collected in the four Barangays (Bunga, San Pablo, Dinarawan and San Roque) of which each area consists of 30 samples. To identify morphological variations in the leaf blade shape of water hyacinth, digital imaging was prepared and the acquired images were loaded into tpsDig2 program. Using thin-plate spline (TPS) series, landmark analysis was completed and subjected to symmetry and asymmetry in geometric data (SAGE) software. Results in Procrustes ANOVA showed high significant differences (P less than 0.0001) in the two factors analyzed: the sides and the individuals by sides which denoting high fluctuating asymmetry. This could be inferred that asymmetric variability might be associated to the outcomes of fluctuating asymmetry that have been derived from genetic and non-genetic influences. Moreover, differences of leaf blade shape have been observed from the collected leaf samples and among the study areas. Thus, using geometric morphometric analysis enables to identify morphological variations within and among species of the same taxa.
- Finding maximum flow in the network: A Matlab program and
application
Authors: WenJun Zhang.Computational Ecology; Software,2018,8(2:57-61
Abstract: Maximum flow problems are expected occurring in some biological networks. As early as in 1950s, Ford and Fulkcerson proposed an algorithm to find maximum flow in a network. In this study I presented the full codes of Ford-Fulkcerson algorithm and given an application example.
- Disparity in the pronotal shapes between sexes in the two populations of
Brontispa longissima (Gestro, 1885) from Caraga region, Philippines using
landmark-based geometric morphometrics
Authors: D. M. Carillo; I.N. dela Cruz.Computational Ecology Software,2018,8(3:62-74
Abstract: The study was conducted to describe the disparity in the pronotal shapes of Brontispa longissima populations in Caraga region, Philippines. Relative warp analysis was utilized for quantifying the shape while Canonical Variance Analysis (CVA) was used to compare shape variation between populations. Results from MANOVA test showed that individual symmetry has high significant values (p less than 0.05). In terms of determining the different variations between populations, pooled males have the p value of 7.62*10^(-15) and pooled females have 8.54*10^(-6), wherein the two values display high significant scores between the two sexes. Moreover, determining the disparity of both sexes from the two geographical locations, Surigao population has the highest p value of 7.63*10^(-15) compared to Agusan population which obtained 6.072*10^(-12), manifesting that populations from the two locations vary in the shape of the pronotum. CVA scatterplot also generates population discrimination indicating the presence of sexual dimorphism in pronotal shapes, while biogeographical factor may affect the shape structure in the pronotum of B. longissima.
- Evaluation of the sustainable urban development in the Mashhad Metropolis
using Ecological Footprint Method
Authors: Q. Haghparast; Ahmadizadeh, Javad Dawoudian.Computational Ecology Software,2018,8(3:75-87
Abstract: The footprint analysis approach is based on the idea that a certain amount of land will be required in one or more environmental domains for the consumption of any commodity or energy in order to ensure the flow of the resources consumed and the disposal of the resulting fossil fuels. So, there are several methods to calculate the sustainability and ecological effects of urban areas. Meanwhile, the method of ecological footprint is a new approach that offers clear and measurable results in urban management. The purpose of this research is to assess the sustainability of Mashhad's metropolis development with ecological footprint indicators in different sectors of consumption, such as housing, transportation, food, goods and services. In this research, all services and goods which are consumed by inhabitants of Mashhad, used throughout their lives, included in six types of land use including land energy, agriculture, pasture, fishery, forest and land, and the per capita footprint of any types of land use. The results of this research show that per capita ecological footprint of every person in Mashhad is 1.27 average of world hectare. Considering the bio capacity in the study area (0.66 hectares), facing ecological deficit and meeting the needs of its inhabitants, according to the population of 3.135.618, an area equivalent to 3,982,235 hectares is needed to respond their habitants. That is almost twice the living capacity of the region. It indicates the Mashhad Metropolitan dependence on supporting areas to meet the needs of its inhabitants.
- What is RSS
Abstract: RSS is a means of receiving content across the internet without having to visit websites directly. When you see the RSS tag on a web page, then you know that site offers an RSS feed. You may download a RSS reader (e.g., at http://www.iaees.org/tools/RSSOwl-java.zip). Install it on your computer and create a new folder, and then create a new feed with a RSS feed address, e.g., http://www.iaees.org/publications/journals/ces/rss.xml, then set something. Any update of RSS feed site will automatically reach your RSS reader. If you have subscribed an online journal by RSS, journal contents or articles will reach you once the latest issue is available or the latest article is published.
- Computational Ecology and Software
Authors: International Academy of Ecology; Environmental Sciences
Abstract: Computational Ecology and Software (ISSN 2220-721X) is an open access, peer-reviewed online journal that considers scientific articles in all different areas of computational ecology (http://www.iaees.org/publications/journals/ces/ces.asp; http://www.iaees.org/publications/journals/ces/online-version.asp). It is the transactions of the International Society of Computational Ecology (http://www.iaees.org/societies/isce/isce.asp). The journal is concerned with the ecological researches, constructions and applications of theories and methods of computational sciences including computational mathematics, computational statistics and computer science. It features the simulation, approximation, prediction, recognition, and classification of ecological issues. Intensive computation is one of the major stresses of the journal. The journal welcomes research articles, short communications, review articles, perspectives, and book reviews. The journal also supports the activities of the International Society of Computational Ecology. The topics to be covered by CES include, but are not limited to: (1) Computation intensive methods, numerical and optimization methods, differential and difference equation modeling and simulation, prediction, recognition, classification, statistical computation (Bayesian computing, randomization, bootstrapping, Monte Carlo techniques, stochastic process, etc.), agent-based modeling, individual-based modeling, artificial neural networks, knowledge based systems, machine learning, data exploration, network analysis and computation, databases, ecological modeling and computation using Geographical Information Systems, satellite imagery, and other computation intensive theories and methods. (2) Artificial ecosystems, artificial life, complexity of ecosystems and virtual reality. (3) The development, evaluation and validation of software and algorithms for computational ecology. The development and evaluation of apparatus, instruments and machines for ecological and environmental analysis, investigation and monitoring based on the software of computational ecology. (4) Methodological applications of computational ecology in the researches of ecology and environmental sciences.
Authors can submit their works to the email box of this journal, ces@iaees.org. All manuscripts submitted to CES must be previously unpublished and may not be considered for publication elsewhere at any time during review period of this journal. In addition to free submissions from authors around the world, special issues are also accepted. The organizer of a special issue can collect submissions (yielded from a research project, a research group, etc.) on a specific topic, or submissions of a conference for publication of special issue.
- Using data clustering as a method of estimating the risk of establishment
of bacterial crop
Authors: Watts MJ. Computational Ecology; Software,2011,1(1:1-13
Abstract: Previous work has investigated the use of data clustering of regional species assemblages to estimate the relative risk of establishment of insect crop pest species. This paper describes the use of these techniques to estimate the risk posed by bacterial crop plant diseases. Two widely-used clustering algorithms, the Kohonen Self-Organising Map and the k-means clustering algorithm, were investigated. It describes how a wider variety of SOM architectures than previously used were investigated, and how both of these algorithms reacted to the addition of small amounts of random noise to the species assemblages. The results indicate that the k-means clustering algorithm is much more computationally efficient, produces better clusters as determined by an objective measure of cluster quality and is more resistant to noise in the data than equivalent Kohonen SOM. Therefore k-means is considered to be the better algorithm for this problem.
- Are individual based models a suitable approach to estimate population
vulnerability' - a case study
Authors: Griebeler EM. Computational Ecology; Software,2011,1(1:14-24
Abstract: European populations of the Large Blue Butterfly Maculinea arion have experienced severe declines in the last decades, especially in the northern part of the species range. This endangered lycaenid butterfly needs two resources for development: flower buds of specific plants (Thymus spp., Origanum vulgare), on which young caterpillars briefly feed, and red ants of the genus Myrmica, whose nests support caterpillars during a prolonged final instar. I present an analytically solvable deterministic model to estimate the vulnerability of populations of M. arion. Results obtained from the sensitivity analysis of this mathematical model (MM) are contrasted to the respective results that had been derived from a spatially explicit individual based model (IBM) for this butterfly. I demonstrate that details in landscape configuration which are neglected by the MM but are easily taken into consideration by the IBM result in a different degree of intraspecific competition of caterpillars on flower buds and within host ant nests. The resulting differences in mortalities of caterpillars lead to erroneous estimates of the extinction risk of a butterfly population living in habitat with low food plant coverage and low abundance in host ant nests. This observation favors the use of an individual based modeling approach over the deterministic approach at least for the management of this threatened butterfly.
- Analysis of some experimental time series by Gause: application of simple
mathematical models
Authors: Nedorezov LV. Computational Ecology; Software,2011,1(1:25-36
Abstract: For the approximation of some of well-known time series of Paramecia aurelia and Paramecia caudatum (under the separated cultivation of both species) population size changing in time, some well-known models were used. For all considering models values of parameters were estimated with least square method (with global fitting) in two different ways: with and without additional limits for parameter values. In the case without additional limits for model parameters deviations between theoretical (model) trajectories and experimental time series were tested for Normality (Kolmogorov-Smirnov test, and Shapiro-Wilk test) with zero average, and for existence/absence of serial correlation (Durbin-Watson criteria). The best results were observed for Gompertz and Verhulst models. Under the assumption that parameter K (maximum value of population size) is greater than all elements of initial sample the best results were observed for Gompertz model. In the last case the canonical technique for analysis of set of deviations can be applied in restricted form and needs in further development. In such a situation we cannot test the set of deviations on Normality with zero average (for big samples) because after a certain time moment all experimental points will be at one side of theoretical curve; at this situation we have to have a serial correlation in the sequence of deviations, etc.
- Simulation of arthropod abundance from plant composition
Authors: Zhang WJ. Computational Ecology; Software,2011,1(1:37-48
Abstract: The relationship between arthropod abundance and plant composition is extremely complex. It is very hard to develop a mechanistic model to describe the relationship. This study aimed to simulate arthropod abundance from plant composition on grassland using an artificial neural network developed by the author, and to compare simulation performances between the neural network and conventional models. The results revealed that there were complex interactions between plants and arthropods, and the arthropod abundance on grassland was significantly determined of plant families and their cover-degrees rather than plant species and their cover-degrees. Neural network exhibited a better simulation performance than multivariate regression and response surface model. Cross validation indicated that prediction performance of neural network was also superior to these models. It was concluded that neural network is an effective tool to model arthropod abundance from plant composition on grassland. A moderate dimensionality for input space may be determined to produce a reasonably trained neural network. Such procedures for dimensionality reduction as PCE, etc., were suggested being used in the data treatment in neural network modeling. A high dimensionality for input space and a few samples in the input set would result in the deficient learning of neural network. Randomization procedure for sample submission would help to eliminate the sequence correlation but may result in a worse performance in simulation and prediction. It was suggested that randomization procedure could be used to the sample submission for these situations with a lot of samples and a lower dimensionality.
- Evaluating a Bayesian approach to improve accuracy of individual
photographic identification methods using ecological distribution data
Authors: Stafford R; Lloyd JR. Computational Ecology Software,2011,1(1:49-54
Abstract: Photographic identification of individual organisms can be possible from natural body markings. Data from photo-ID can be used to estimate important ecological and conservation metrics such as population sizes, home ranges or territories. However, poor quality photographs or less well-studied individuals can result in a non-unique ID, potentially confounding several similar looking individuals. Here we present a Bayesian approach that uses known data about previous sightings of individuals at specific sites as priors to help assess the problems of obtaining a non-unique ID. Using a simulation of individuals with different confidence of correct ID we evaluate the accuracy of Bayesian modified (posterior) probabilities. However, in most cases, the accuracy of identification decreases. Although this technique is unsuccessful, it does demonstrate the importance of computer simulations in testing such hypotheses in ecology.
- Fuzzy cognitive maps outmatch loop analysis in dynamic modeling of
ecological systems
Authors: Ferrarini A. Computational Ecology; Software,2011,1(1:55-59
Abstract: Modeling natural systems is challenging due to their complexity in terms of variables, interactions, and dynamics. Much of this complexity is rooted in the existence of multiple ways through which acting variables affect each other. Besides the simple direct effects, numerous indirect effects emerge in ecological systems. Through an illustrative example, I exemplify here several advantages of fuzzy cognitive maps (FCM) over loop analysis (LA) in dynamic modeling of ecological systems. In addition to being able to incorporate information about the magnitude of variables interactions, FCM can make predictions about multiple simultaneous perturbations. Furthermore, FCM allow for the simulation of different magnitude of initial perturbations to the system. Last, FCM estimate the amount of variable increase/decrease, not just the likely direction of change. Hence, even if LA is still much more used than FCM in the scientific literature, FCM can be considered fitter than LA in modeling ecological systems.
- Quantitative risk analysis and prediction of potential distribution areas
of common lantana (Lantana Camara) in China
Authors: Lui XR. Computational Ecology; Software,2011,1(1:60-65
Abstract: The ornamental hybrid shrub, Lantana camara L. (lantana), is a serious environmental weed and has been targeted for the biologist. This paper used such approaches as Analytic Hierarchy Process (AHP), fuzzy decision, etc., to analyze and predict potential distribution areas of common lantana in 147 sites of China. Based on ecological properties of common lantana, we chose 5 climate ecological factors, i.e., mean annual temperature, mean temperature from March to May in a year, elevation, days with temperature greater than 25C and annual precipitation. The results showed that common lantana will continue to spread forward north China (Hunan, Hubei, etc.).
- Computational Ecology: an emerging ecological science
Authors: Zhang WJ. Computational Ecology; Software,2011,1(1:66-67
Abstract: Computational ecology is an emerging science to integrate and synthesize computation intensive areas in ecology. It was clearly defined and described in an earlier study. Aims and scope of computational ecology are further refined in present discussion.
- Computational Ecology: Artificial Neural Networks and Their Applications
Authors: Zheng H. Computational Ecology; Software,2011,1(1:68
Abstract: A book, Computational Ecology: Artificial Neural Networks and Their Applications, published in 2010, was introduced and reviewed. This book provides readers with deep insights on algorithms, codes, and applications of artificial neural networks in ecology. A science discipline, computational ecology, is clearly defined and outlined in the book.
- Combined use of weather forecasting and satellite remote sensing
information for fire risk, fire and fire impact monitoring
Authors: Wolfgang Knorr; Ioannis Pytharoulis, George P. Petropoulos, Nadine Gobron. Computational Ecology Software,2011,1(2:112-120
Abstract: The restoration of fire-affected forest areas needs to be combined with their future protection from renewed catastrophic fires, such as those that occurred in Greece during the 2007 summer season. The present work demonstrates that the use of various sources of satellite data in conjunction with weather forecast information is capable of providing valuable information for the characterization of fire danger with the purpose of protecting the Greek national forest areas. This study shows that favourable meteorological conditions have contributed to the fire outbreak during the days of the unusually damaging fires in Peloponnese as well as Euboia (modern Greek: Evia) at the end of August 2007. During those days, Greece was located between an extended high pressure system in Central Europe and a low pressure system in the Middle East. Their combination resulted in strong north-northeasterly winds in the Aegean Sea. As a consequence, strong winds were also observed in the regions of Evia and Peloponnese, especially in mountainous areas. The analysis of satellite images showing smoke emitted from the fires corroborates the results from the weather forecasts. A further analysis using the Fraction of Absorbed Photosyntetically Active Radiation (FAPAR) as an indicator of active vegetation shows the extent of the destruction caused by the fire. The position of the burned areas coincides with that of the active fires detected in the earlier satellite image. Using the annual maximum FAPAR as an indicator of regional vegetation density, it was found that only regions with relatively high FAPAR were burned.
- Detecting ecological breakpoints: a new tool for piecewise regression
Authors: Alessandro Ferrarini. Computational Ecology; Software,2011,1(2:121-124
Abstract: Simple linear regression tries to determine a linear relationship between a given variable X (predictor) and a dependent variable Y. Since most of the environmental problems involve complex relationships, X-Y relationship is often better modeled through a regression where, instead of fitting a single straight line to the data, the algorithm allows the fitting to bend. Piecewise regressions just do it, since they allow emphasize local, instead of global, rules connecting predictor and dependent variables. In this work, a tool called RolReg is proposed as an implementation of Krummel's method to detect breakpoints in regression models. RolReg, which is freely available upon request from the author, could useful to detect proper breakpoints in ecological laws.
- Wavelet analysis to detect regime shifts in animal movement
Authors: C. Gaucherel. Computational Ecology; Software,2011,1(2:69-85
Abstract: Animals most often move in a non-homogeneous way as a long movement path through a heterogeneous landscape that corresponds to a sequence of various behavioural states. Hence, a large majority of movement analyses make the assumption that long movements combine typical behaviours like intensive search or resting which are separated by sharp transitions. This study aimed at providing an alternative method for identifying intensive search areas using sharp as well as more continuous (smooth) transitions. I proposed analyzing movement data over temporal and spatial scales by the use of the wavelet analysis and drew inferences about the behaviours that shape movements. I computed a synthetic index built with wavelet time-spectra of turning angle and speed parameters, this method offered a robust and automatic way to characterize movement transitions. The first step was to work on simulated movements to define the confidence levels of detection. The second was to illustrate the use of wavelet analysis on the movements of wandering albatrosses. As a result, this study outlined two fundamental areas of interest in animal movement analysis: i) it is relevant to select behavioural modes with continuous transitions between them along the animal's movement, as it is done with usual segmentation methods; ii) to suppose that every behaviour and every transition between them is intrinsically multiscale (i.e. with a scaling property) appeared to be an interesting approach to identify and characterize them. The mathematical robustness and predictive ability of wavelet analysis make it a promising road towards multiscale movement ecology that fuses insights from the study of animal behaviour and environmental properties.
- About a modification of Beddington-Free-Lawton model of parasite-host
system dynamics
Authors: P.V. Ivanchikov; L.V. Nedorezov. Computational Ecology Software,2011,1(2:86-94
Abstract: Current publication is devoted to the construction of modification of well-known Beddington - Free - Lawton model of parasite - host system dynamics and its analysis. In basic model and in modified model there is one and the same assumption that under the determined values of sizes of interacting populations number of attacked hosts is determined by Poisson' law. In modified model it was took into account that hosts, which were attacked two or more times by parasites, die, and it doesn't lead to the increase of parasite population size. For modified model population dynamic regimes and structure of the space of model parameters are analyzed.
- Use of geospatial technology in evaluating landscape cover type changes in
Chandoli National Park, India
Authors: Ekwal Imam. Computational Ecology; Software,2011,1(2:95-111
Abstract: Monitoring changes in landscape cover types has been a great concern for forest and wildlife managers. Both managers find it very important to know how much area is suitable for wildlife species and what areas are affected due to anthropogenic pressure. To address these concerns, evaluation of Chandoli National Park was done to see the changes that have taken place over the past 28 years. The National Park is situated in India lying within 170 04' 00" N to 170 19' 54" N and 730 40' 43" E to 730 53' 09" E. Remotely sensed data procured from satellite IRS-P6, LISS-III (2005) was used. The satellite data was digitally processed and collateral data were generated from topographic maps. The comparative analysis of topographic-map and imagery of 1977 and 2005 revealed that 120.9 km2 of evergreen forest has been lost during 28 years. Contrary to this an increase of 51.15 km2 in scrubland and 64.19 km2 in grasslands were noted. Furthermore, forest cover and land use maps of the study area were prepared from satellite data using supervised maximum likelihood classification technique. The study reveals that Park supports diversified habitats of scrubland (27.47%), grassland (20.13%), rejuvenated (22.17%) and evergreen forest (16.07%). The diversified cover types and improvement in forest density has made the Park suitable for wild animals than the previous one when it was not declared as protected area. The study advocates that if a forest area is protected and conserved from anthropogenic pressure may become more suitable for wild animals.
- Measuring competition in plant communities where it is difficult to
distinguish individual plants
Authors: Christian Damgaard. Computational Ecology; Software,2011,1(3:125-137
Abstract: A novel method for measuring plant-plant interactions in undisturbed semi-natural and natural plant communities where it is difficult to distinguish individual plants is discussed. It is assumed that the ecological success of the different plant species in the plant community may be adequately measured by plant cover and vertical density (a measure that is correlated to the 3-dimensional space occupancy and biomass). Both plant cover and vertical density are measured in a standard pin-point analysis in the beginning and at the end of the growing season. In the outlined competition model the vertical density at the end of the growing season is assumed to be a function of the cover of all species at the start of the growing season, and the cover at the start of the growing season is assumed to be a function of the vertical density of all species at the end of the previous growing season. The method allows direct measurements of the competitive effects of neighbouring plants on plant performance and the estimation of parameters that describe the ecological processes of plant-plant interactions during the growing season as well as the process of survival and recruitment between growing seasons. Additionally, the presented method is suited for testing different ecological hypothesis on competitive interactions along environmental gradients, investigating the importance of competition, as well as predicting the likelihood of different ecological scenarios.
- Improving cluster-based methods for investigating potential for insect
pest species establishment: region-specific risk factors
Authors: Michael J. Watts; Susan P. Worner. Computational Ecology Software,2011,1(3:138-145
Abstract: Existing cluster-based methods for investigating insect species assemblages or profiles of a region to indicate the risk of new insect pest invasion have a major limitation in that they assign the same species risk factors to each region in a cluster. Clearly regions assigned to the same cluster have different degrees of similarity with respect to their species profile or assemblage. This study addresses this concern by applying weighting factors to the cluster elements used to calculate regional risk factors, thereby producing region-specific risk factors. Using a database of the global distribution of crop insect pest species, we found that we were able to produce highly differentiated region-specific risk factors for insect pests. We did this by weighting cluster elements bytheir Euclidean distance from the target region. Using this approach meant that risk weightings were derived that were more realistic, as they were specific to the pest profile or species assemblage of each region. This weighting method provides an improved tool for estimating the potential invasion risk posed by exotic species given that they have an opportunity to establish in a target region.
- Complexity analysis in particulate matter measurements
Authors: Luciano Telesca; Michele Lovallo. Computational Ecology Software,2011,1(3:146-152
Abstract: We investigated the complex temporal fluctuations of particulate matter data recorded in London area by using the Fisher-Shannon (FS) information plane. In the FS plane the PM10 and PM2.5 data are aggregated in two different clusters, characterized by different degrees of order and organization. This results could be related to different sources of the particulate matter.
- Some aspects of animal behavior and community dynamics
Authors: Vikas Rai; R. K. Upadhyay, S. N. Raw, Nitu Kumari. Computational Ecology Software,2011,1(3: 153-182
Abstract: We simulate the dynamical behavior of a few two - dimensional predator - prey systems in two - dimensional parameter spaces to gain insight into how functional responses affect community dynamics. The insight gained helps us design three dimensional systems. We construct models for a few ecosystems with three species and study them using computer simulations. The models have been developed by linking food chains which have both kinds of predators: specialist as well as generalist. The linking functions are weakly non-linear. The three dimensional model ecosystems have sexually reproducing top - predators. We perform extensive simulations to figure out dynamics of dynamical possibilities caused by changes in animal behavior. The animals change the foraging strategies and behave differently in different environments. At the end of the paper, we examine how diseases can govern transitions in meandering of dynamical models in bounded volume of their phase spaces.
- A Java program for non-parametric statistic comparison of community
structure
Authors: WenJun Zhang. Computational Ecology; Software,2011,1(3: 183-185
Abstract: The Java algorithm to statistically compare structure difference of two communities was presented in this study. Euclidean distance, Manhattan distance, Pearson correlation, Point correlation, quadratic correlation and Jaccard coefficient were included in the algorithm. The algorithm was used to compare rice arthropod communities in Pearl River Delta, China, and the results showed that the family composition of arthropods for Guangzhou, Zhongshan, Zhuhai, and Dongguan are not significantly different.
- A new fuzzy algorithm for ecological ranking
Authors: Alessandro Ferrarini. Computational Ecology; Software,2011,1(3: 186-188
Abstract: Ecological ranking is a prerequisite to many kinds of environmental decisions. It requires a set of 'objects' (e.g., competing sites for species reintroduction, or competing alternatives of environmental management) to be evaluated on the basis of multiple weighted criteria, and then ranked from the best to the worst, or vice versa. The resulting ranking is then used to choose the course of an action (e.g., the optimal sites where a species can be reintroduced, or the optimal management scenario for a protected area). In this work, a new tool called FuzRnk is proposed as a modification of classic fuzzy algorithm. FuzRnk, which is freely available upon request from the author, allows for a fuzzy ranking of GIS objects (e.g., landscape patches or zones within protected areas). With respect to classic fuzzy algorithm, FuzRnk introduces two modifications: a) criteria can be weighted on the basis of their importance, b) not only the best performances, but also the worst ones are considered in the ranking procedure.
- Estimating critical abundance thresholds in exploited populations: a
simulation approach based on species resilience to disturbance
Authors: Rishi Sharma; Scott W. Raborn. Computational Ecology Software, 2011, 1(4:189-207
Abstract: Managers of exploited species too often assume that populations can be maintained at equilibrium abundances that will provide maximum yield. Most evidence to date suggests that populations seldom adhere to equilibria, but rather fluctuate stochastically between bounds. The last decade has revealed the consequences of not incorporating uncertainty around point estimates of equilibria, which has led to the decline of several fisheries. We used the sample importance re-sampling (SIR) algorithm to exhibit the uncertainties in point estimates generated by models for management of two Chinook salmon Oncorhynchus tshawytscha stocks and a bowhead whale Balaena mysticetus population. We then incorporated the cumulative uncertainties of each system into a simulation technique similar to population viability analyses (PVA) to provide decision support for establishing threshold abundances of each exploited population. The simulation presented was based upon the resilience (time to recover from perturbations to abundance) of each population, which was found to be relatively high for the Chinook stocks and low for bowhead whale. Various thresholds could be chosen depending on: (1) how much time should be allowed for the population to recover from a perturbation, (2) when should the stock be considered recovered (i.e., within 1%, 5%, 10%, and so on of what abundance would be had there been no perturbation), and (3) the maximum allowable risk that a threshold is too low. Reasonable thresholds for the Chinook stocks were 60% to 80% of abundances that provide maximum sustained yield (SMSY). Due to their low productivity, no clear threshold below the biomass point estimate was apparent for bowhead whale.
- About a dynamic model of interaction of insect population with food plant
Authors: L.V. Nedorezov. Computational Ecology; Software, 2011, 1(4:208-217
Abstract: In present paper there is the consideration of mathematical model of food plant (resource) - consumer (insect population) - pathogen system dynamics which is constructed as a system of ordinary differential equations. The dynamic regimes of model are analyzed and, in particular, with the help of numerical methods it is shown that trigger regimes (regimes with two stable attractors) can be realized in model under very simple assumptions about ecological and intra-population processes functioning. Within the framework of model it was assumed that the rate of food flow into the system is constant and functioning of intra-population selfregulative mechanisms can be described by Verhulst model. As it was found, trigger regimes are different with respect to their properties: in particular, in model the trigger regimes with one of stable stationary points on the coordinate plane can be realized (it corresponds to the situation when sick individuals in population are absent and their appearance in small volume leads to their asymptotic elimination); also the regimes with several nonzero stationary states and stable periodic fluctuations were found.
- Estimating survival rates in ecological studies with small unbalanced
sample sizes: an alternative Bayesian point estimator
Authors: Christian Damgaard; Adeline Fayolle. Computational Ecology Software, 2011, 1(4:218-223
Abstract: Increasingly, the survival rates in experimental ecology are presented using odds ratios or log response ratios, but the use of ratio metrics has a problem when all the individuals have either died or survived in only one replicate. In the empirical ecological literature, the problem often has been ignored or circumvented by different, more or less ad hoc approaches. Here, it is argued that the best summary statistic for communicating ecological results of frequency data in studies with small unbalanced samples may be the mean of the posterior distribution of the survival rate. The developed approach may be particularly useful when effect size indexes, such as odds ratios, are needed to compare frequency data between treatments, sites or studies.
- Comparison of numerical simulations of reactive transport and
chemostat-like models
Authors: I. Haidar; F. Gerard, A. Rapaport. Computational Ecology Software, 2011, 1(4:224-239
Abstract: The objective of the paper is to evaluate the ability of reactive transport models and their numerical implementations (such as MIN3P) to simulate simple microbial transformations in conditions of chemostat or gradostat models, that are popular in microbial ecology and waste treatment ecosystems. To make this comparison, we first consider an abstract ecosystem composed of a single limiting resource and a single microbial species that are carried by advection. In a second stage, we consider another microbial species in competition for the same limiting resource. Comparing the numerical solutions of the two models, we found that the numerical accuracy of simulations of advective transport models performed with MIN3P depends on the evolution of the concentrations of the microbial species: when the state of the system is close to a non-hyperbolic equilibrium, we observe a numerical inaccuracy that may be due to the discretization method used in numerical approximations of reactive transport equations. Therefore, one has to be cautious about the predictions given by the models.
- A fitter use of Monte Carlo simulations in regression models
Authors: Alessandro Ferrarini. Computational Ecology; Software, 2011, 1(4:240-243
Abstract: In this article, I focus on the use of Monte Carlo simulations (MCS) within regression models, being this application very frequent in biology, ecology and economy as well. I'm interested in enhancing a typical fault in this application of MCS, i.e. the inner correlations among independent variables are not used when generating random numbers that fit their distributions. By means of an illustrative example, I provide proof that the misuse of MCS in regression models produces misleading results. Furthermore, I also provide a solution for this topic.
- Computer generation of initial spatial distribution for cell automata
Authors: GuangHua Liu; WenJun Zhang. Computational Ecology Software, 2011, 1(4:244-248
Abstract: The algorithm to generate spatial distribution patterns was developed and presented in this study. Three typical spatial distribution patterns, i.e., Poisson distribution, binomial distribution, and negative binomial distribution were included in the algorithm. The Java program was also provided. The algorithm can be used to generate initial distribution in cell automata modeling.
- Spatiotemporal pattern induced by self and cross-diffusion in a spatial
Holling-Tanner model
Authors: Ranjit Kumar Upadhyay; N. K. Thakur.Computational Ecology Software,2012,2(1:1-25
Abstract: In this paper, we have made an attempt to provide a unified framework to understand the complexspatiotemporal patterns induced by self and cross diffusion in a spatial Holling-Tanner model forphytoplankton-zooplankton-fish interaction. The effect of critical wave length which can drive the system toinstability is investigated. We have examined the criterion between two cross-diffusivity (constant and timevarying)on the stability of the model system and for diffusive instability to occur. Based on these conditionsand by performing a series of extensive simulations, we observed the irregular patterns, stationary strips, spots,and strips-spots mixture patterns. Numerical simulation results reveal that the regular strip-spot mixturepatterns prevail over the whole domain on increasing the values of self- diffusion coefficients of phytoplanktonand zooplankton and the dynamics of the system do not undergo any further changes.
- System dynamic approach for management of urban parks: a case study
Authors: Lucia Tamburino; Valentina La Morgia, Ezio Venturino.Computational Ecology Software,2012,2(1:26-41
Abstract: Public agencies tackling the issues of natural resource management need objective analysis to anticipate theecosystem consequences of their actions. Mathematical models can be regarded as an effective tool to supportdecision makers in this context because of their predictive capacity and of their ability to describe complexnatural systems. In particular, the aim of this paper is to show how mathematical modelling and simulation canbe applied in the field of urban park management. As an example, we consider a case study where a domesticherbivore, the sheep, was introduced as a natural regulator of grass growth. The results show that theintroduction of sheep is not currently sustainable and that it should be complemented by other measures inorder to tackle both the issue of regulating grass growth and to prevent debarking of the newly planted trees.
- About a modification of May model of parasite-host system dynamics
Authors: P.V. Ivanchikov; L.V. Nedorezov.Computational Ecology Software,2012,2(1:42-52
Abstract: Current publication is devoted to the construction of modification of well-known May model of parasite - hostsystem dynamics and its analysis. In basic model and in modified model there is one and the same assumptionthat under the determined values of sizes of interacting populations number of attacked hosts is determined bybinomial law. In modified model it was took into account that hosts, which were attacked two or more timesby parasites, die, and it doesn't lead to the increase of parasite population size. For modified model populationdynamic regimes and structure of the space of model parameters are analyzed.
- Assessing ballast treatment standards for effect on rate of establishment
using a stochastic model of the green crab
Authors: Cynthia Cooper; Carlton D. Hunt, Cheryl Dingus, P. Scott Libby, Greg Kirkbride.Computational Ecology Software,2012,2(1:53-69
Abstract: This paper describes a stochastic model used to characterize the probability/risk of NIS establishment fromships' ballast water discharges. Establishment is defined as the existence of a sufficient number of individualsof a species to provide for a sustained population of the organism. The inherent variability in populationdynamics of organisms in their native or established environments is generally difficult to quantify. Muchqualitative information is known about organism life cycles and biotic and abiotic environmental pressures onthe population, but generally little quantitative data exist to develop a mechanistic model of populations insuch complex environments. Moreover, there is little quantitative data to characterize the stochasticfluctuations of population size over time even without accounting for systematic responses to biotic and abioticpressures. This research applies an approach using life-stage density and fecundity measures reported inresearch to determine a stochastic model of an organism's population dynamics. The model is illustrated withdata from research studies on the green crab that span a range of habitats of the established organism and werecollected over some years to represent a range of time-varying biotic and abiotic conditions that are expectedto exist in many receiving environments. This model is applied to introductions of NIS at the IMO D-2 and theU.S. ballast water discharge standard levels designated as Phase Two in the United States Coast Guard'sNotice of Proposed Rulemaking. Under a representative range of ballast volumes discharged at U.S. ports, theaverage rate of establishment of green crabs for ballast waters treated to the IMO-D2 concentration standard(less than 10 organisms/m3) is predicted to be reduced to about a third the average rate from untreated ballast waterdischarge. The longevity of populations from the untreated ballast water discharges is expected to be reducedby about 90% by treatment to the IMO-D2 concentration standard.
- Using artificial neural networks to predict the distribution of bacterial
crop diseases from biotic and abiotic factors
Authors: Michael J. Watts; Susan P. Worner.Computational Ecology Software,2012,2(1:70-79
Abstract: Constructing accurate computational global distribution models is an important first step towards the understanding of bacterial crop diseases and can lead to insights into the biology of disease-causing bacteria species. We constructed artificial neural network models of the geographic distribution of six bacterial diseases of crop plants. These ANN modelled the distribution of these species from regional climatic factors and from regional assemblages of host crop plants. Multiple ANN were combined into ensembles using statistical methods. Tandem ANN, where an ANN combined the outputs of individual ANN, were also investigated. We found that for all but one species, superior accuracies were attained by methods that combined biotic and abiotic factors. These combinations were produced by both ensemble and cascaded ANN. This shows that firstly, ANN are able to model the geographic distribution of bacterial crop diseases, and secondly, that combining abiotic and biotic factors is necessary to achieve high modelling accuracies. The work reported in this paper therefore provides a basis for constructing models of the distribution of bacterial crop diseases.
- A program for statistic test of community evenness
Authors: WenJun Zhang; Hao Zheng.Computational Ecology Software,2012,2(1:80-82
Abstract: A Java program to statistically test community evenness was developed in this study. In the algorithm the community diversity was represented by Shaanon-Wiener index, and Ewens-Caswell neutrality model was used to test community evenness. The algorithm was used to test the evenness of four arthropod communities in Pearl River Delta, China. The results showed that all communities were not even.
- Modeling and analysis of some methods of entomological data collection
Authors: L.V. Nedorezov.Computational Ecology; Software,2012,2(2:83-95
Abstract: In current publication the stochastic model of individual migrations within the limits of closed domain andprocesses of data collections using in entomology are considered. The behavior of data variation with respectto changing of population size is analyzed. In particular, it was shown that dependence of standard deviationshas a non-linear character under the population density increasing. It was also shown that confidence level todatasets of population density which were obtained with traditional methods and under the low value ofpopulation density must be extremely low.
- Improving Eastern Bluebird nest box performance using computer analysis of
satellite images
Authors: Sarah Svatora; Lior Shamir.Computational Ecology Software,2012,2(2:96-102
Abstract: Bird conservationists have been introducing man-made boxes in an effort to increase the bluebird population.In this study we use computer analysis of satellite images to show that the performance of the boxes used byEastern Bluebirds (Sialia sialis) in Michigan can be improved by about 48%. The analysis is based on a strongcorrelation found between the edge directionality measured in the satellite image of the area around the box,and the preferences of the birds when selecting their nesting site. The method is based on satellite images takenfrom Google Earth, and can be used by conservationists to select a box placement strategy that will optimizethe efficacy of the boxes deployed in a given area.
- Permutation tests to estimate significances on Principal Components
Analysis
Authors: Vasco M. N. C. S. Vieira.Computational Ecology; Software,2012,2(2:103-123
Abstract: Principal Component Analysis is the most widely used multivariate technique to summarize information in adata collection with many variables. However, for it to be valid and useful the meaningful information must beretained and the noisy information must be sorted out. To achieve it an index from the original data set isestimated, after which three classes of methodologies may be used: (i) the analytical solution to the distributionof the index under the assumption the data has a multivariate normal distribution, (ii) the numerical solution tothe distribution of the index by means of permutation tests without any assumption about the data distributionand (iii) the bootstrap numerical solution to the percentiles of the index and the comparison to its assumedvalue for the null hypothesis without any assumption about the data distribution. New indices are proposed tobe used with permutation tests and compared with previous ones from application to several data sets. Theiradvantages and draw-backs are discussed together with the adequacy of permutation tests and inadequacy ofboth bootstrap techniques and methods that rely on the assumption of multivariate normal distributions.
- Dynamical complexities in a discrete-time food chain
Authors: Abd-Elalim A. Elsadany.Computational Ecology; Software,2012,2(2:124-139
Abstract: In this paper, a discrete-time food chain characterized by three species is modeled by a system of threenonlinear difference equations. The existence and local stability of the equilibrium points of the discretedynamical system are analyzed. It is shown that for some parameter values the interior equilibrium point losesits stability through a discrete Hopf bifurcation. Basic properties of the discrete system are analyzed by meansof phase portraits, bifurcation diagrams and Lyapunov exponents. We have varied the result through numericalcalculation.
- A novel approach for modeling malaria incidence using complex categorical
household data: The minimum message length (MML) method applied to
Indonesian data
Authors: Gerhard Visser; Pat Dale, David Dowe, Ermi Ndoen, Mike Dale, Neil Sipe.Computational Ecology Software,2012,2(3:140-159
Abstract: We investigated the application of a Minimum Message Length (MML) modeling approach to identify thesimplest model that would explain two target malaria incidence variables: incidence in the short term and onthe average longer term, in two areas in Indonesia, based on a range of ecological variables includingenvironmental and socio-economic ones. The approach is suitable for dealing with a variety of problems suchas complexity and where there are missing values in the data. It can detect weak relations, is resistant to overfittingand can show the way in which many variables, working together, contribute to explaining malariaincidence. This last point is a major strength of the method as it allows many variables to be analysed. Datawere obtained at household level by questionnaire for villages in West Timor and Central Java. Data werecollected on 26 variables in nine categories: stratum (a village-level variable based on the API/AMI categories),ecology, occupation, preventative measures taken, health care facilities, the immediate environment, householdcharacteristics, socio-economic status and perception of malaria cause. Several models were used and thesimplest (best) model, that is the one with the minimum message length was selected for each area. The resultsshowed that consistent predictors of malaria included combinations of ecology (coastal), preventative (cleanbackyard) and environment (mosquito breeding place, garden and rice cultivation). The models also showedthat most of the other variables were not good predictors and this is discussed in the paper. We conclude thatthe method has potential for identifying simple predictors of malaria and that it could be used to focus malariamanagement on combinations of variables rather than relying on single ones that may not be consistentlyreliable.
- A fuzzy mathematics approach in measuring air pollution from motor
vehicles
Authors: Soumak Biswas; Sripati Jha, Ramayan Singh.Computational Ecology Software,2012,2(3:160-168
Abstract: Air pollution from motor vehicle in cities specially in developing countries has been a major source of urbanair pollution and hence a cause of concern for the administrators of the cities as well as for researchers in thefield of ecology and mathematics. In the present work, the fuzzy membership functions for some of theattributes regarding air pollution from motor vehicle are proposed. To study the index of air pollution indifferent area of a city, the air pollution index is proposed, which takes into account the membership functionfor the attributes of pollution. By applying a suitable interpolation formula (in our case Lagrange's interpolation formula) a polynomial curve is obtained, which gives the measure of air pollution at any point ofthe city under certain assumptions. The effectiveness and suitability of the method is established by taking anexample.
- Chaos and bifurcation of a nonlinear discrete prey-predator system
Authors: Abd-Elalim A. Elsadany; H. A. EL-Metwally, E. M. Elabbasy, H. N. Agiza.Computational Ecology Software,2012,2(3:169-180
Abstract: The discrete-time Prey-predator system obtained by two dimensional map was studied in present study. Thefixed points and their stability were analyzed. Bifurcation diagram has been obtained for selected range ofdifferent parameters. As some parameters varied, the model exhibited chaos as a long time behavior. Lyapunovexponents and fractal dimension of the chaotic attractor of our map were also calculated. Complex dynamicssuch as cycles and chaos were observed.
- Bayesian parameter estimation in dynamic population model via particle
Markov chain Monte Carlo
Authors: Meng Gao; XingHua Chang, XinXiu Wang.Computational Ecology Software,2012,2(4:181-197
Abstract: In nature, population dynamics are subject to multiple sources of stochasticity. State-space models (SSMs) provide an ideal framework for incorporating both environmental noises and measurement errors into dynamic population models. In this paper, we present a recently developed method, Particle Markov Chain Monte Carlo (Particle MCMC), for parameter estimation in nonlinear SSMs. We use one effective algorithm of Particle MCMC, Particle Gibbs sampling algorithm, to estimate the parameters of a state-space model of population dynamics. The posterior distributions of parameters are derived given the conjugate prior distribution. Numerical simulations showed that the model parameters can be accurately estimated, no matter the deterministic model is stable, periodic or chaotic. Moreover, we fit the model to 16 representative time series from Global Population Dynamics Database (GPDD). It is verified that the results of parameter and state estimation using Particle Gibbs sampling algorithm are satisfactory for a majority of time series. For other time series, the quality of parameter estimation can also be improved, if prior knowledge is constrained. In conclusion, Particle Gibbs sampling algorithm provides a new Bayesian parameter inference method for studying population dynamics.
- Fluctuations of population dynamics model parameters: View on the problem
of climate change
Authors: L. V. Nedorezov.Computational Ecology; Software,2012,2(4:198-212
Abstract: In current publication the statistical method of analysis of population time series in considered. This method is based on analysis of dynamics of non-linear ecological model parameter estimations in time, and devoted to investigation of influence of change of weather conditions on population dynamics (on the other words, it is devoted to analysis of climate change from the standpoint of separated population dynamics). Estimations of model parameters were obtained for parts (which contains 12 values each) of initial sample. For the approximation of sub-samples the well-known Kostitzin model of population size changing in time was used. It was used for the approximation of dataset of pine looper moth (Bupalus piniarius L.) dynamics in Germany (total sample size is 58). Estimation of model parameters were obtained with known least squares method. Analyses of tendencies of model parameter estimations showed that there are no reasons for rejecting hypotheses about the equalities of regression line angles to zero. It gives the base for conclusion about the absence of serious change in weather conditions in Germany during analyzing time interval (60 years).
- WORTHY: a new model for ecological ranking and evaluation
Authors: Alessandro Ferrarini.Computational Ecology; Software,2012,2(4:213-219
Abstract: Ecological ranking and environmental decision making require that a set of objects (e.g., competing sites for species introduction, or alternative sites for the allocation of man-made features) are listed from the best to the worst one. The resulting ranking is then used to choose which actions to implement; worse and intermediate solutions are immediately excluded, while optimal and sub-optimal solutions are taken into account, discussed and then applied. In this paper, WORTHY is presented as a new model for ecological ranking and evaluationof competing alternatives based on a set of weighted criteria. I have developed WORTHY model with the goal of employing a TOPSIS-like algorithm for worthy solutions in situations of environmental and ecological conflict management. Compared to TOPSIS algorithm, WORTHY allows to: a) decide the type of normalization, b) build an user-defined decision function, c) perform what-if analysis and d) sensitivity analysis.
- Synthetic Aperture Radar (SAR) images features clustering using Fuzzy
c-means (FCM) clustering algorithm
Authors: Rashid Hussain.Computational Ecology; Software,2012,2(4:220-225
Abstract: Remote sensing applications such as Ecological monitoring, Disaster monitoring, Volcanic monitoring, surveillance and reconnaissance requires broad range imaginary data with very high resolution. Data captured under different times such as day or night and under different weather conditions poses adverse affects on retrieved results. Synthetic Aperture Radar (SAR) technology is used to mitigate such adverse effects. Recently SAR technology re-emerges because of the decrease in the cost of electronic components and tremendous advancement in computing power. This paper provides an application of Fuzzy c-means (FCM) clustering algorithm to SAR Images. The objective of this study is to segment various region of interest inremote sensing images for ecological monitoring.
- The role of aerosols to increase rainfall in the regions with less
intensity rain: A modeling study
Authors: Shyam Sundar; Rajan K. Sharma.Computational Ecology Software,2013,3(1:1-8
Abstract: In this paper, we established an ecological type three-dimensional nonlinear mathematical model to study the effect of aerosol particles in increasing rainfall in the regions of less intensity rain. The phenomenon of nonlinearity is based on the concepts of ecology related to growth rate, death rate and interaction process (Smith, 1974). It is assumed that clouds are formed in the atmosphere but are not able to develop uninterrupted rainfall. The rainfall can be enhanced by introducing aerosol particles conducive to raindrops formation from cloud droplets. It is shown that the intensity of rainfall increases as the concentration of externally introduced aerosols and the density of cloud droplets increases. The numerical simulation has also been performed tosupport analytical results.
- Evaluation of land use/land cover changes in Mekelle City, Ethiopia using
Remote Sensing and GIS
Authors: Mary Tahir; Ekwal Imam, Tahir Hussain.Computational Ecology Software,2013,3(1:9-16
Abstract: Land use is a dynamic phenomenon that changes with time and space due to anthropogenic pressure and development. Evaluating the existing land use and its periodic change is useful for urban planners, policy makers and natural resource managers. Land use and land cover changes in Mekelle City, Ethiopia (north east Africa) over a period of 25 years was studied using remotely sensed data. Multi temporal satellite data of Landsat was used to map and monitor urban land use changes occurred during two point of time of 1985 and 2010. A pixel base supervised image classification was used to map land use land cover classes for maps of both time set. A positive changes of 200% was recorded in urban features of Mekelle, whereas, an area of 6 square km was added in grasslands. On the other hand a loss of 92.86% was estimated in bare land and all farm lands available in the area were converted into other feature and it declined from 3 square km to nil. Since forest land is protected so that no change in sparse forest was recorded.
- Landscape Builder: Software for the creation of initial landscapes for
LANDIS from FIA data
Authors: William Dijak.Computational Ecology; Software,2013,3(2:17-25
Abstract: I developed Landscape Builder to create spatially explicit landscapes as starting conditions for LANDIS Pro 7.0 and LANDIS II landscape forest simulation models from classified satellite imagery and Forest Inventory and Analysis (FIA) data collected over multiple years. LANDIS Pro and LANDIS II models project future landscapes by simulating tree growth, tree species succession, disease, insects, fire, wind, and management disturbance. Landscape Builder uses inventory plot attributes from the FIA inventory database, FIA unit map, National Forest type map, National Forest size class map, land cover map, and landform map to assign FIA plot attributes to raster pixels representing a real forest landscape. In addition to creating a detailed map of current (initial) forest landscape conditions, the software produces specific files required for use in LANDIS Pro 7.0 or LANDIS II format. Other tools include the ability to create a dominant species and age-class map from previously created LANDIS maps, a tool to create a dominant species and age-class map from a stand map and field plot data, and a tool to convert between Esri ascii rasters and Erdas file format types.
- MBI: an R package for calculating multiple-site beta diversity indices
Authors: YouHua Chen.Computational Ecology; Software,2013,3(2:26-32
Abstract: Beta diversity is one of most important features in community ecology. Indices for pairwise comparison of beta diversity have been extensively developed, but the ones specifically designed for multiple-site comparison of beta diversity are still limited. Currently, by compiling all the available metrics based on the previous literature, plus some new metrics developed in the present report, we made the calculation of these multiplesite beta-diversity statistics become ready for ecologists using R computing environment. An empirical study was present using 290 real-world presence/absence matrices. The results showed that (1) mean pairwise indices could be good surrogates for multiple-site indices in principle, except the mean pairwise richness different index; (2) most of the indices were highly correlated, as indicated by Pearson correlation and significance test. The new R package "MBI" for calculating multiple-site diversity indices could be downloaded from the http://cran.r-project.org/web/packages/MBI/.
- An ecological type nonlinear model for the removal of carbon dioxide from
the atmosphere by introducing liquid species
Authors: Shyam Sundar.Computational Ecology; Software,2013,3(2:33-43
Abstract: The average temperature of our planet is increasing in past several decades due to emission of global warming gases such as CO2, CH4, etc. in the atmosphere leading to undesirable environmental consequences. Therefore, it is necessary to find a mechanism by which a global warming gas can be removed from the regional atmosphere. In this paper, therefore, we proposed an ecological type nonlinear mathematical model for the removal of a global warming gas CO2 from the regional atmosphere by externally introduced liquid species, which may react with this gas and removed it by gravity. The model consists of three dependent variables namely; the concentration of carbon dioxide, the concentration of externally introduced liquid species and the concentration of particulate matters (secondary species) formed due to interaction of carbon dioxide with liquid species. The local and global stability conditions are discussed using Routh-Hurwitz criteria and suitable Lyapunove's function respectively. It is shown, analytically and numerically, that the concentration of carbon dioxide decreases as the rate of introduction of externally introduced liquid species increases.
- Estimating significances of differences between slopes: A new methodology
and software
Authors: Vasco M. N. C. S. Vieira; Joel Creed.Computational Ecology Software,2013,3(3:44-52
Abstract: Determining the significance of slope differences is a common requirement in studies of self-thinning, ontogeny and sexual dimorphism, among others. This has long been carried out testing for the overlap of the bootstrapped 95% confidence intervals of the slopes. However, the numerical random re-sampling with repetition favours the occurrence of re-combinations yielding largely diverging slopes, widening the confidence intervals and thus increasing the chances of overlooking significant differences. To overcome this problem a permutation test simulating the null hypothesis of no differences between slopes is proposed. This new methodology, when applied both to artificial and factual data, showed an enhanced ability to differentiate slopes.
- Fractal basins in an ecological model
Authors: I. Djellit; S. Chouit.Computational Ecology Software,2013,3(3:53-60
Abstract: Complex dynamics is detected in an ecological model of host-parasitoid interaction. It illustrates fractalization of basins with self-similarity and chaotic attractors. This paper describes these dynamic behaviors, bifurcations, and chaos. Fractals basins are displayed by numerical simulations.
- Machine learning algorithms for predicting roadside fine particulate
matter concentration level in Hong Kong Central
Authors: Yin Zhao; Yahya Abu Hasan.Computational Ecology Software,2013,3(3:61-73
Abstract: Data mining is an approach to discover knowledge from large data. Pollutant forecasting is an important problem in the environmental sciences. This paper tries to use data mining methods to forecast fine particles (PM2.5) concentration level in Hong Kong Central, which is a famous business centre in Asia. There are several classification algorithms available in data mining, such as Artificial Neural Network (ANN) and Support Vector Machine (SVM). ANN and SVM are both machine learning algorithm used in variant area. This paper builds PM2.5 concentration level predictive models based on ANN and SVM by using R packages. The data set includes 2008-2011 period meteorological data and PM2.5 data. The PM2.5 concentration is divided into 2 levels: low and high. The critical point is 40ug/cubic meter (24 hours mean), which is based on the standard of US Environmental Protection Agency (EPA). The parameters of both models are selected by multiple cross validation. According to 100 times 10-fold cross validation, the testing accuracy of SVM is around 0.803-0.820, which is much better than ANN whose accuracy is around 0.746-0.793.
- Computing the uncertainty associated with the control of ecological and
biological systems
Authors: Alessandro Ferrarini.Computational Ecology; Software,2013,3(3:74-80
Abstract: Recently, I showed that ecological and biological networks can be controlled by coupling their dynamics to evolutionary modelling. This provides numerous solutions to the goal of guiding a system's behaviour towards the desired result. In this paper, I face another important question: how reliable is the achieved solution' In other words, which is the degree of uncertainty about getting the desired result if values of edges and nodes were a bit different from optimized ones' This is a pivotal question, because it's not assured that while managing a certain system we are able to impose to nodes and edges exactly the optimized values we would need in order to achieve the desired results. In order to face this topic, I have formulated here a 3-parts framework (network dynamics - genetic optimization - stochastic simulations) and, using an illustrative example, I have been able to detect the most reliable solution to the goal of network control. The proposed framework could be used to: a) counteract damages to ecological and biological networks, b) safeguard rare and endangered species, c) manage systems at the least possible cost, and d) plan optimized bio-manipulations.
- Dynamics of pine hawkmoth (Hyloicus pinastri L.): Search for stationary
dynamical regime
Authors: L.V. Nedorezov.Computational Ecology; Software,2013,3(4:81-90
Abstract: In current publication possible population dynamics regimes are analyzed using pre-model statistical method. Method was applied to well-known pine hawkmoth (Hyloicus pinastri L.) time series (Schwerdtfeger, 1944, 1968). Provided statistical analysis showed that observed dynamics of pine hawkmoth doesn't correspond to strong 2-, 3-,..., or 9-year cycles which can be generated by one-dimensional discrete models, and doesn't correspond to fluctuations near stable level.
- Bootstrap estimation of resource selection probability functions
Authors: Sandra V. Cardozo; Bryan F. J. Manly, Raydonal Ospina, Carlos T. S. Dias.Computational Ecology Software,2013,3(4:91-101
Abstract: Resource selection functions (RSFs) are used for quantify how animals are selective in the use of the habitat period or food. A Resource Selection Probability Function (RSPF) can be estimated if N, the total number of units in the population, and n1 the total number of used units in the study period are both known and small. An approximation of the RSPF can then be estimated using any standard program for logistic regression but the variances of the estimates of the parameters are too small. Three methods of bootstrap sampling, parametric, nonparametric and a modified parametric method are proposed for the estimation of variances, with a discussion about the limitations of logistic regression for estimating RSPF. The method for estimating the RSPF described here has potential applications in medicine, ecology and other areas.
- Significances of differences between slopes: An upgrade for replicated
time series
Authors: Vasco M. N. C. S. Vieira; Joel Creed.Computational Ecology Software,2013,3(4:102-109
Abstract: In some ecology subjects the slope of the line fit between x and y variables is the focus of concern. Such is the case of self-thinning theory, developed for plant demography and later verified also occurring in algae and animals. Different slopes identify statistical populations subject to different conditions. Therefore, it is fundamental that a test is able to identify honestly significant differences between slopes. The most used tested for the overlap of the 95% confidence intervals of the bootstrapped slopes. However, Vieira and Creed (2013) demonstrated it to possess weak theoretical grounds having proposed a permutation methods alternative. Unfortunately, both were fallible upon small sample sizes and/or large data scatter. Data about self-thinning, as well as other subjects, often comes in replicated time series enabling upgrading the test algorithm to randomize sampling units only within the respective time frame. This was added to the previous software, increasing outstandingly the capacity of the permutation test in identifying both true and false differences between slopes.
- A comparative study of a system of Lotka-Voltera type of PDEs through
perturbation methods
Authors: H. A. Wahab; M. Shakil, T. Khan, S. Bhatti, M. Naeem.Computational Ecology Software,2013,3(4:110-125
Abstract: In this paper the Adomian Decomposition Method (ADM) is employed in order to solve linear and nonlinear functional equations and the results are then compared with those produced by Homotopy Perturbation Method (HPM) through a system of Lotka Voltera type of PDEs. The result produced by HPM are promising and ADM appears as a special case of HPM for Lotka Voltera type of PDEs.
- Ecological significance of core, buffer and transition boundaries in
biosphere reserve: A remote sensing study in Similipal, Odisha, India
Authors: Anima Biswal; A Jeyaram, Sumit Mukherjee, Umesh Kumar.Computational Ecology Software,2013,3(4:126-137
Abstract: Protected areas and national parks need periodic assessment and monitoring for evaluating natural resources, effectiveness of management and studying the effects of global climate change. The present work has been undertaken to prepare the multi-date vegetation density maps in terms of Normalised vegetation index (NDVI) and to monitor the changes in and around the areas close to transition, buffer and core boundaries of Similipal Biosphere Reserve (SBR) using digital remote sensing and GIS techniques.Time series Landsat images covering a period of 30 years are used for change detection studies.
- Analysis of complex wetland ecological system: Effect of harvesting
Authors: Nilesh Kumar Thakur; Rashi Gupta.Computational Ecology Software,2017,7(4:140-152
Abstract: In this paper, we have studied interaction among diffusive phytoplankton, zooplankton and fish population with Beddington-DeAngelis type functional response for the zooplankton and Holling type III for fish. The stability analysis of the model system with diffusion and without diffusion has been analyzed. The conditions for Maximum sustainable yield and Optimal harvesting policy for non-spatial model have been discussed. Our study may be helpful to improve and manage ecosystem services provided by wetlands on an agricultural landscapes include fisheries, water conservation, climate change and many more.
- Period-doubling bifurcation and chaos control in a discrete-time mosquito
model
Authors: Qamar Din; Muhammad Asif Khan.Computational Ecology Software,2017,7(4:153-166
Abstract: This article deals with the study of some qualitative properties of a discrete-time mosquito Model. It is shown that there exists period-doubling bifurcation for wide range of bifurcation parameter for the unique positive steady-state of given system. In order to control the bifurcation we introduced a feedback strategy. For further confirmation of complexity and chaotic behavior largest Lyapunov exponents are plotted.
- Elliptic Fourier Analysis of body shape variation of Hippocampus spp.
(seahorse) in Danajon Bank, Philippines
Authors: S. R. M. Tabugo-Rico; L.A. Tumanda, C.K. Cabrido, C.M. Apale, E. Dumalagan.Computational Ecology Software,2017,7(4:167-178
Abstract: Seahorses inhabit various ecosystems hence, had become a flagship species of the marine environment. The Philippines as a hot spot of biodiversity in Asia holds a number of species of seahorses. This serve as an exploratory study to describe body shape variation of selected common seahorse species: Hippocampus comes, Hippocampus histrix, Hippocampus spinosissimus and Hippocampus kuda from Danajon bank using Elliptic Fourier Analysis. The method was done to test whether significant yet subtle differences in body shape variation can be species-specific, habitat-influenced and provide evidence of sexual dimorphism. It is hypothesized that phenotypic divergence may provide evidence for genetic differentiation or mere adaptations to habitat variation. Results show significant considerable differences in the body shapes of the five populations based on the canonical variate analysis (CVA) and multivariate analysis of variance (MANOVA) with significant p values. Populations were found to be distinct from each other suggesting that body shape variation is species-specific, habitat-influenced and provided evidence for sexual dimorphism. Results of discriminant analysis show further support for species specific traits and sexual dimorphism. This study shows the application of the method of geometric morphometrics specifically elliptic fourier analysis in describing subtle body shape variation of selected Hippocampus species.
- Application of DSSAT crop model for wheat crop growth simulation in some
wheat growing districts of northern India
Authors: Anima Biswal; Bhabhana Sahay, KV Ramana, MVR Sesha Sai.Computational Ecology Software,2017,7(4:179-187
Abstract: Process based Crop growth simulation models are being used as a potential decision support tool for informed decision making by policy makers and researchers. Calibration and validation of a crop growth simulation model is the fundamental process before applying the model projections to a new location. CERES crop growth simulation model has been used by a number of researchers worldwide to simulate wheat growth. This study is undertaken to calibrate and validate CERES model on DSSAT (Decision Support System for Agro Technology Transfer) platform for six predominantly wheat growing districts of Northern India.
- Some dynamic models for development of insecticide resistance in insect
population
Authors: WenJun Zhang; GuiLu Zhang.Computational Ecology Software,2018,8(1:1-6
Abstract: In present study, we proposed a fundamental model for development of insecticide resistance in insect population, which comprises two differential equations and an algebraic equation: dx/dt = r1(c, t) x - f1(c, t) x + g1(c, t) y - a(c, t) x y; dy/dt = r2(c, t) y - g2(c, t) y + f2(c, t) x - b(c, t) x y; c = u(t). where t: time (insect generation, year, etc.); x(c, t): resistant subpopulation at t; y(c, t): susceptible subpopulation at t; c: dosage / concentration of the insecticide. Two special models for election theory and induce variation theory were derived from the fundamental model. We provided the solution of the model and analyzed some of the model behavior. Resistant strength was proposed based on the model, which is positively related to the common used resistance indices, e.g., LC50. Finally, an alternative model, revised from Lotka-Volterra competition model was given. The mechanism of formation and development of insecticide resistance may change with various factors including insect species and environmental conditions. The present models are expected to provide a fundamental for further research.
- A simple mathematical model of mosquito's dynamics at stationary
environmental conditions
Authors: L.V. Nedorezov; J.J. Yermekbayeva, A.N. Omarov, B.N. Nedorezova.Computational Ecology Software,2018,8(1:7-14
Abstract: Mathematical model of population dynamics with two types of individuals (mosquitoes which are malaria transmission vectors, and mosquitoes which are not transmission vectors) is under consideration. Some of basic properties of model were determined. Numerical analysis allowed obtaining typical dynamic regime.
- Nocturnal flights lead to collision risk with power lines and wind farms
in Lesser Kestrels: a preliminary assessment through GPS tracking
Authors: Marco Gustin; Giuseppe Giglio, Stefania C. Pellegrino, Annagrazia Frassanito, Alessandro Ferrarini.Computational Ecology Software,2018,8(1:15-22
Abstract: We present here the first report about Lesser Kestrels' flight height behaviour and potential collision risk with wind farms and power lines in two colonies (Gravina in Puglia and Altamura; Apulia, Italy) that present the highest density of Lesser Kestrels worldwide in urban areas. Using accurate GPS data-loggers on nine Lesser Kestrels, we collected data on flight activities during the nestling period. The tracked Lesser Kestrels spent 50% of the monitoring time at heights above ground level (AGL) lower than 41 m, and 75% of time below 98 m AGL. Flight heights resulted not significantly different between the two colonies. Instead, at night Lesser Kestrels resulted to fly at significantly lower altitudes than in the daytime. Our findings, although preliminary, underline the potential collision risk with power lines and wind farms at night in the Lesser Kestrels' colony of Gravina in Puglia. Instead, collision risk resulted negligible during the daytime for both colonies. We conclude that the disappearing of pseudo-steppes in the study area is forcing Lesser Kestrels to flight also at night for foraging purposes during the breading season, which in turn leads to an increased risk of collision with power lines and wind farms.
- Morphotypes of cone snails (Conus mustelinus), Conidae: a phenetic
analysis
Authors: S. R. M. Tabugo; S.R. Boco, S.I.G Masangcay, J.D. Anunciado, C.M.Q. Pao.Computational Ecology Software,2018,8(1:23-31
Abstract: This study describes phenotypic differentiation of Conus mustelinus, a gastropod species belonging to Family Conidae through phenetic analysis. There exist a number of morphotypes for this species. Thus, it is valuable to look into the nature and variation of this species. In this study, adult shell color polymorphism was observed and six (6) morphotypes were documented and described. Herewith, M5 and M6 among the morphotypes studied, closely resembled each other. A total of 27 characters were used to construct the character matrix. The important characters were spiral ground color, spiral bands color, body whorl color, band between subshoulder plus central band and aperture coloration. The generated phenogram revealed possible clusters based on overall phenotypic similarity. Describing variation and relationships based on a combination of discrete shell morphological characters proved to be pertinent in identification process thereby, addressing sibling species and cryptic speciation.
- Fuzzy modeling for the spread of influenza virus and its possible
control
Authors: Renu Verma; S.P. Tiwari, Ranjit Kumar Upadhyay.Computational Ecology Software,2018,8(1:32-45
Abstract: In this paper, we analyze a model of Influenza spread with an asymptotic transmission rate, wherein the disease transmission rate and death rate are considered as fuzzy sets. Comparative studies of the equilibrium points of the disease for the classical and fuzzy models are performed. Using the concept of probability measure and fuzzy expected value, we obtain the fuzzy basic reproduction number for groups of infected individuals with different virus loads. Further, a basic reproduction number for the classical and the fuzzy model are compared. Finally, a program based on the basic reproduction value of disease control is suggested and the numerical simulations are carried out to illustrate the analytical results.
- Analysis of variance: Comfortless questions
Authors: L.V. Nedorezov.Computational Ecology; Software,2017,7(3:91-99
Abstract: In this paper the simplest variant of analysis of variance is under consideration. Three examples from textbooks by Lakin (1990) and Rokitsky (1973) were re-considered. It was obtained that traditional one-way ANOVA and Kruskal - Wallis criterion can lead to unreal results about factor's influence on value of characteristics. Alternative way to solution of the same problem is under consideration too.
- Effect of automobiles on global warming: A modeling study
Authors: Shyam Sundar; Ashish Kumar Mishra, Ram Naresh.Computational Ecology Software,2017,7(3:100-108
Abstract: Global warming threatens our environment as well as basic human needs. In the present scenario, increasing demand and excessive use of automobiles have increased the level of carbon dioxide emission in the environment, providing a significant contribution to increase the global warming. This paper deals with the modeling of the effect of automobiles on global warming. For this, three nonlinearly interacting variables namely; density of human population, density of automobiles and the concentration of carbon dioxide have been taken into account. In the modeling process, it is assumed that the density of automobiles increases in proportion to human population following a logistic growth. The model is analyzed using stability theory of ordinary differential equations. Local and global stability conditions are established to study the feasibility of the model system. It is shown that with increase in human population, the demand for automobiles increases which has significant effect on global warming increase.
- WORMSPREAD: an individual-based model of invasive earthworm population
dynamics
Authors: George W. Armstrong; Ahsan Mahmood, Andie Nugent, Sonya Dexter, Emily Hutto, Timothy S. McCay, Ahmet Ay.Computational Ecology Software,2017,7(3:109-122
Abstract: Invasive earthworm species, such as Lumbricus rubellus, can cause changes to forest soils, which may result in reduced forest biodiversity. Individual Based Modeling (IBM) offers a way to predict the spread of invasive species and can provide insight for control. We developed an individual-based, spatially explicit, earthworm population dynamics modeling software package (WORMSPREAD). This software accounts for environmental interactions and individual variation that impact population growth and behavior of earthworms. In the model, individual earthworms are affected by temperature and pH, resulting in changes in reproduction, growth, movement and mortality. WORMSPREAD allows ecologists and conservation biologists to test invasion scenarios with simulations that involve variations in landscape structure and demographic parameters that potentially affect abundance and distribution of invasive earthworm species. The user interface is easy to learn and flexible enough to incorporate new data. Results can help determine where to concentrate conservation efforts and control strategies. An example study of the spread of L. rubellus in a portion of the Adirondack Park in upstate New York demonstrates computational experiments that can be conducted with WORMSPREAD. WORMSPREAD can be used to predict population growth in real landscapes, with real variation in environmental conditions. However, it will only lead to accurate predictions if the underlying physiological and behavioral traits of the invading species are known. Indeed, our assessment of these traits for L. rubellus indicates that more data are needed for this species, and the situation is likely to be more challenging for less well-studied species. Thus we encourage more studies that relate the physiology and behavior of invasive species to variability of environmental conditions in invaded habitats.
- Describing shell shape variations and sexual dimorphism of Golden Apple
Snail, Pomacea caniculata (Lamarck, 1822) using geometric morphometric
analysis
Authors: C.C. Cabuga; Jr., R.P. Sularte, M.C.O. Acob, M.M.P. Eleazar, C.M.T. Tiempo, C.C.D. Joseph, M.K.A.Angco, A.M.N. Calub, H.C. Havana, J.D. Dominguito, M.L.M. Budlayan, R.M.A. Colon, J.R.Guilleno, S.M. Arriza.Computational Ecology Software,2017,7(3:123-139
Abstract: Pomacea caniculata or Golden Apple Snail (GAS) existed to be a rice pest in the Philippines and in Asia. Likewise, geographic location also contributes its increasing populations thus making it invasive among freshwater habitats and rice field areas. This study was conducted in order to describe shell shape variations and sexual dimorphism among the populations of P. caniculata. A total of 180 were randomly collected in the three lakes of Esperanza, Agusan del Sur (Lake Dakong Napo, Lake Oro, and Lake Cebulan), of which each lake comprised of 60 samples (30 males and 30 females). To determine the variations and sexual dimorphism in the shell shape of golden apple snail, coordinates was administered to relative warp analysis and the resulting data were subjected to Multivariate Analysis of Variance (MANOVA), Principal Component Analysis (PCA) and Canonical Variate Analysis (CVA). The results show statistically significant (P less than 0.05) from the appended male and female dorsal and ventral/apertural portion. While male and female spire height, body size, and shell shape opening also shows significant variations. These phenotypic distinctions could be associated with geographic isolation, predation and nutrient component of the gastropods. Thus, the importance of using geometric morphometric advances in describing sexual dimorphism in the shell shape of P. caniculata.
- Comparative growth models of big-scale sand smelt (Atherina boyeri Risso,
1810) sampled from Hirfanll Dam Lake, Klrsehir, Ankara, Turkey
Authors: S. Benzer; R. Benzer.Computational Ecology Software,2017,7(2):82-90
Abstract: In this current publication the growth characteristics of big-scale sand smelt data were compared for population dynamics within artificial neural networks and length-weight relationships models. This study aims to describe the optimal decision of the growth model of big-scale sand smelt by artificial neural networks and length-weight relationships models at Hirfanll Dam Lake, Klrsehir, Turkey. There were a total of 1449 samples collected from Hirfanll Dam Lake between May 2015 and May 2016. Both model results were compared with each other and the results were also evaluated with MAPE (mean absolute percentage error), MSE (mean squared error) and r2 (coefficient correlation) data as a performance criterion. The results of the current study show that artificial neural networks is a superior estimation tool compared to length-weight relationships models of big-scale sand smelt in Hirfanll Dam Lake.
- MATASS: the software for multi-attribute assessment problems
Authors: WenJun Zhang.Computational Ecology; Software,2017,7(2):38-48
Abstract: In present study, we developed the software for multi-attribute assessment problems, MATASS (Multi-Attribute Assessment System). The procedures of MATASS include, (1) for a multi-attribute assessment problem, there are m attributes for the assessment of n objects (ecosystems, networks, or habitats, etc.), and each attribute is given a weight according to its importance, and each of the attributes, according to its attribute domain, is assigned to one of seven common types, i.e., interval, upper limit, lower limit, weakly determined value, strongly determined value, no upper and lower limits (the bigger the better), and no upper and lower limits (the smaller the better); (2) data matrix is normalized corresponding to the types of attributes; (3) find the objects that do not meet their specified attribute intervals or values, disqualify these objects and remove them from object list, and the remaining objects are identified as the qualified; (4) re-normalize the data matrix for the qualified objects; (5) assess the qualified objects using various multi-attribute assessment methods, like TOPSIS, REVAWEA, SAWA, etc; (6) determine the final ranking of the qualified objects using Copeland method. Full Matlab codes and software of MATASS were given.
- Site selection of wind power plant using multi-criteria decision-making
methods in GIS: A case study
Authors: E. Chamanehpour; Ahmadizadeh, Akbarpour.Computational Ecology Software,2017,7(2):49-64
Abstract: Wind energy due to abundance, minimal environmental pollution and high cost-effectiveness are considered as one of the best clean energies. One of the most important issues in the use of wind energy is the correct layout of suitable extraction locations of wind energy to generate electricity. The suitablesite selection to establish wind power plants based on the principles and criteria of a sustainable environmental advancement which in addition to cost-effectiveness and employment generation results in a cheap and inexhaustible energy source besides providing the basic information to attract domestic as well as foreign investments to use the wind energy. In the present study, 16 information layer consisting of: wind speed, temperature, altitude, slope, towns, villages, main and secondary routes, airport, protected areas, land use, rivers, wells, springs and aqueducts, earthquake acceleration and faults was considered as the basic decision-making criteria. Using multi-criteria decision-making methods in GIS environment viz. Analytical Hierarchy Process (AHP) and Fuzzy methods, modelling of the suitable extraction sites of wind energy was carried out. The results exhibited that the best regions that can be nestled in the excellent class include Zirkouh of Ghaen, east of Darmian, east of Sarbishe, north of Khoosf and east of Deyhouk. Considering the calculations of the present study, from the total case study area, 3.3% in AHP method and 4.5% in Fuzzy method had excellent potential to use wind energy. Finally, the area located in the north-west of Khoosf was proposed as the best area to establish the wind power plant.
- Landmark based geometric morphometric analysis describing sexual
dimorphism in wings of Neurothemis terminata (Ris, 1911) from Mt.
Hilong-Hilong, Philippines
Authors: C.C. Cabuga; Jr., L.A.Estano, J.J. Z. Abelada, I.N. B. dela Cruz, M.K.A. Angco, C.C. D. Joseph, J.P. M. Gamallo, J.E.O. Lador, H.C. Havana, P.J.A. Martinez.Computational Ecology Software,2017,7(2):65-81
Abstract: Landmark-based geometric morphometric analysis describing sexual dimorphism in wings of Neurothemis terminata (Ris, 1911) from Mt. Hilong-Hilong, Remedios Trinidad Romualdez, Agusan del Norte, Philippines was applied in selected female and male populations. A total of 30 females and 30 males were collected and subjected to landmark- based analysis. To demonstrate the variation in wing morphology, landmark data was employed to relative warp analysis and the resulting scores were analyzed using Multivariate Analysis of Variance (MANOVA), Principal Component Analysis (PCA) and Canonical Variate Analysis (CVA). The result shows significant differences (P less than 0.05) between the appended female and male populations. The obtained result indicates that each sexes of N. terminata displays morphological difference in wings which may be attributed to the sexual selection, flight performance and flapping kinematics.
- A new model to describe the relationship between species richness and
sample size
Authors: WenJun Zhang.Computational Ecology; Software,2017,7(1):1-7
Abstract: In the sampling of species richness, the number of newly found species declines as increase of sample size, and the number of distinct species tends to an upper asymptote as sample size tends to the infinity. This leads to a curve of species richness vs. sample size. In present study, I follow my principle proposed earlier (Zhang, 2016), and re-develop the model, y=K(1-e^(-rx/K)), for describing the relationship between species richness (y) and sample size (x), where K is the expected total number of distinct species, and r is the maximum variation of species richness per sample size (i.e., max dy/dx). Computer software and codes were given.
- Comparative fluctuating asymmetry of spotted barb (Puntius binotatus)
sampled from the Rivers of Wawa and Tubay, Mindanao, Philippines
Authors: C.C. Cabuga Jr.; R.R.Q. Apostado, J.J.Z. Abelada, L.B. Calagui, C.J. R. Presilda, M.K.A.Angco, J.L. Bual, J. E. O. Lador, J.H. Jumawan, J.C. Jumawan, H.C. Havana, E.A. Requieron, M.A.J. Torres.Computational Ecology Software,2017,7(1):8-27
Abstract: Fluctuating Asymmetry (FA) commonly uses to evaluate environmental stress and developmental variability of different biotic elements. This study aims to describe the possible effects of pollutants on the body shapes of spotted barb (Puntius binotatus) with notes of physico-chemical parameters of Wawa River, Bayugan City, Agusan del Sur and Tubay River, Tubay, Agusan del Norte, Philippines. There were a total of 80 samples (40 females and 40 males) collected from each sampling areas. Digital imaging was prepared and the acquired images were loaded into tpsDig2 program. Standard landmarks on fish morphometric were employed. Using thin-plate spline (TPS) series, landmark analysis were completed and subjected to symmetry and asymmetry in geometric data (SAGE) software. Results in Procrustes ANOVA showed high significant differences of (P less than 0.0001) in the three factors analyzed: the individuals; sides; and the interaction of individuals and sides; indicating high fluctuating asymmetry. In Tubay River, the level of asymmetry in females were 79.06% and in males 71.69% while in Wawa River, the level of asymmetry in females were 76.60% and in males 62.64%. Therefore, indicating high level of asymmetry denotes environmental alterations. On the other hand, physicochemical parameters were also determined in the two sampling areas. The results of One-way ANOVA showed that the mean parameters in Wawa River has significant difference of (P less than 0.0001), while Tubay River has no significant difference. Results of Pearson-correlation of fluctuating asymmetry between physicochemical parameters shows no correlation which suggests that water components is not directly influenced by the fluctuating asymmetry. The approach of FA and physico-chemical parameters were significant for evaluating environmental condition as well as species state of well-being.
- An approximate solution for a generalized Hirota-Satsom coupled (Kdv)
equation
Authors: H.A. Wahab; Rafi Ullah, Saira Bhatti, M. Shahzad, M. Naeem, Fawad Hussain, Sarfraz Ahmad.Computational Ecology Software,2017,7(1):28-37
Abstract: In this paper the Homotopy Analysis Method (HAM), is applied to find the approximate solution of Hirota-Satsuma coupled (KdV) equations, which don't need a small parameter for solution. The results obtained by HAM is compared with exact solution, the results divulge that the Homotopy Analysis Method are most accurate, closed and suitable to exact solution of the equation, as compare to Homotopy Perturbation Method. It is predicated that the HAM can be found usually.
- Describing the body shape variation of spotted barb, Puntius binotatus
(Valenciennes 1842) using fluctuating asymmetry from Tubay, Agusan del
Norte, Philippines
Authors: C. J. Presilda; B. J. Hernando, I. N. B. Dela Cruz, C. L. Solania, C.C. Cabuga, Jr., A.L.G. Suico, E.M.B. Cortez, M.J. Dicdican, J. H. Jumawan, J. C. Jumawan, J. Presilda, E.A. Requieron, M.A.J. Torres.Computational Ecology Software,2016,6(4):120-129
Abstract: This study aims to assess the condition of the water ecosystem in Tubay, Agusan del Norte by showing the level of FA on the bilateral symmetry of Puntius binotatus with respect to its sex that is known to be abundant in the area. This will show the status of P. binotatus in Tubay, Agusan del Norte that is known for having a mining activity in the area. Yet, there were no reports in the area that concerns with the developmental instability of P. binotatus and other fish inhabiting in the area using FA. Fluctuating Asymmetry (FA) defined as a subtle random deviation between the left and right side of symmetrically bilateral organisms that measures the inability of organisms to maintain homeostasis or measures the developmental instability of organisms. A total of 200 individuals (100 male and 100 females) were subjected to FA Analysis. Landmark analyses were obtained using Thin - plate Spline (TPS) series with 16 landmarks generated for each sample and loaded into Symmetry and Asymmetry in Geometric Data (SAGE) software. Procrustes ANOVA shows that individual symmetry has no significant difference. Sides and Interaction showed a high significantly difference (P less than 0.0001) which suggest being asymmetrical in the bilateral symmetry of P. binotatus population. The result of Principal Component Analysis (PCA) shows a level of asymmetry with 77% in female and 73% in the male. FA in female fish can be seen in snout tip, anterior and posterior insertion of the dorsal fin, midpoint, or lateral line, dorsal base of pelvic fin, and dorsal base of pectoral fin. In male samples, affected landmarks can be seen in the anterior and posterior insertion of the dorsal fin, dorsal insertion of caudal fin and dorsal base of the pelvic fin. The level of FA specifies a good indicator of stressors in the environment that causes a decline in reproduction and population.
- Structural control of ecological and biological networks
Authors: Alessandro Ferrarini.Computational Ecology; Software,2016,6(4):130-138
Abstract: Evolutionary Network Control (ENC) allows the control of any kind of ecological and biological network, with an arbitrary number of nodes and links. In this work, ENC has been further expanded to incorporate the structural control of any kind of ecological and biological network. The rationale behind Structural ENC is that during field experiments and manipulations it could result difficult to quantitatively control stocks and flows in order to drive the ecological or biological network towards the desired state. In these cases, similar results can be achieved using a more parsimonious approach based on the inhibition of one or several nodes and/or edges. Although network control through the inhibition of one or several nodes and/or edges is a kind of structural control that acts impolitely if compared to the functional control previously used by ENC, it is more parsimonious from a feasibility (i.e. in situ application) viewpoint, hence in some cases it could be the most feasible solution for the control of the real networks.
- Regional application of process based biogeochemical model DNDC in
Godavari Sub-basin
Authors: A Biswal; KK Choudhury, P Venkat Raju, MVR Sesha Sai.Computational Ecology Software,2016,6(4):139-149
Abstract: The denitrification decomposition (DNDC) model is a process-based computer simulation model of soil carbon and nitrogen biogeochemistry. The DNDC model is one of the few process-based bio-geo chemical crop simulation models for which both a site-specific mode and a regional mode were developed. For regional mode, a region is presented in a typical Geographic Information System (GIS) consisting of many polygons or grid cells. The database consists of spatially differentiated information of location, climate, soil properties, cropping systems, and farm management practices for each polygon or grid cell for the entire modeled region. An attempt was made to establish the methodology for the estimation of soil greenhouse gas fluxes like CH4, CO2 and N2O on a sub-basin scale.
- Load balancing in distributed framework for frequency based thread
pools
Authors: Sheraz Ahmad; Faisal Bahdur, Faiza Kanwal, Riaz Shah.Computational Ecology Software,2016,6(4):150-164
Abstract: The consequence of load balancing algorithms on a thread pool framework name is distributed load balancing frequency based optimization scheme (LDFBOS) to increase its execution. Load balancing in distributed frequency based thread pool scheme is residential towards the ground of synchronizing overhead crude named LDFBOS in Java that slows down its execution due to framework exchange and synchronizing overhead in nodes, we are demonstrating the contrive and execution of load balancing in distributed frequency based thread pool LDFBOS to does usage from distributed in frequency based thread pool (DFBOS), synchronizing primitives that propose benefits of significant scalable moreover, dynamism. We have got resembled the execution of some schemes by Thread Pool Tester which is a Java application simulator and the consequence have demonstrated that load balancing in distributed frequency based thread pool LDFBOS exceeds preceding DFBOS scheme.
- Quantification of uncertainty in the reliability of migration between
habitat patches
Authors: Ali Muhammad Ali Rushdi; Ahmad Kamal Hassan.Computational Ecology Software,2016,6(3):66-82
Abstract: This paper deals with the quantitative assessment of the unreliability of migration between habitat patches in terms of ecological corridor unreliabilities that are known only with uncertainty. The corridor unreliabilities are treated herein as log-normally distributed random variables, and hence the assessment becomes a doublystochastic one. The paper utilizes the multi-affine nature of the reliability function in deriving exact formulas for the mean and variance of the system unreliability, as well as accurate formulas for its third and fourth central moments. These formulas involve the nominal values of certain partial derivatives. The multi-affine nature is also beneficial in the development of an alternative method that involves powers rather than derivatives. These two analytical methods of moments agree reasonably with one another and with the results of Monte Carlo simulations. Several test cases are considered for typical ecology problems with corridor unreliabilities that have a significant variation in their error (range) factor. Numerical plots obtained yield plausible observations and useful insights.
- A mathematical approach to study stress-related behaviors in captive
golden-bellied capuchins (Sapajus xanthosthernos)
Authors: J. A. Jamielniak; A.G. Garcia.Computational Ecology Software,2016,6(3):83-94
Abstract: Exhibition of stress-related behaviors can be used as a criterion to evaluate the welfare of captive animals. Monitoring animal welfare is important because of ethical and conservation issues. Ethical issues are involved in maintaining animals in an environment similar to nature and conservation issues are related to scientific research and environmental education in zoos. One of the most common captive primates found in Brazilian zoos is the golden-bellied capuchin (Sapajus xanthosternos), recognized by its characteristic head coloration with a black or dark brown cap with dark sideburns and golden chest, belly and upper arms. In this paper, we developed a mathematical model that incorporated Fuzzy Theory to study stress-related behaviors in captive golden-bellied capuchin. We defined ''number of visitors'', ''number of sudden loud sounds inside the zoo'' and ''feeding period'' as input variables and the number of stress-related behaviors observed during a pre-defined time as output variable. We chose Fuzzy Theory because behavioral studies involve imprecision and a fuzzy approach provides the development of algorithms that are able to represent uncertainty inherent in data and can be an advantage in cases where an explicit analytical-process model is not available. We tested the mathematical model by comparing model results to field observations in three zoos from Brazil. This paper has revealed that the fuzzy process is a tool to help studies based on behavioral ecology since the model successfully predicted the number of stress-related behaviors presented by the animals.
- Relative warp analysis in determining morphological variation and sexual
dimorphism between sexes of flathead goby (Glossogobius giuris)
Authors: C.C. Cabuga; Jr., C.B.E. Masendo, B.J.H. Hernando, C.C.D. Joseph, J.P.B. Velasco, M.K.A. Angco, M. A. Ayaton, O.L.P. Obenza, J. H. Jumawan, J.C. Jumawan, E.A. Requieron, M.A.J. Torres, H.C. Havana.Computational Ecology Software,2016,6(3):95-105
Abstract: Landmark-based geometric morphometrics is an effective tool for measuring the biological shape, shape variation and covariation both for biotic and abiotic elements. It ensures graphical illustrations of shape changes that are visually interesting and instinctual. Using the results from relative warp analysis, histograms, CVA and PCA were generated to visualize morphological variations and sexual dimorphism. A total of 60 individuals (30 males and 30 females) were subjected to landmark-based analysis. This application will demonstrate morphological variation and sexual dimorphism on the body shape of Glossogobius giuris using geometric morphometry by means of Relative Warp Analysis. Sixteen landmarks generated 19 relative warps for each sample and showed slight morphological variation were females obtained the highest percentage than males. The MANOVA test value shows non-significant value (P=0.1655) on the left lateral side between sexes. This indicates that there were no shape variations and may be due to behavior and ecology of the organism to compete with others for food haunting, mating and to buffer environmental condition. While the right lateral side shows significant value (P less than 0.05) between sexes this reason explains that they were sexually dimorphic. That was essential for its adaptation and reproduction. The results of Principal Component Analysis (PCA) and Canonical Variance Analysis (CVA) show no significant body variations between sexes. This study was employed to identify the importance or relative warp analysis in detecting and morphological variations and sexual dimorphism of G. giuris collected at Lower Agusan River, Butuan City, Philippines.
- A computational intensive method- Lubrication approximation theory for
blade coating process
Authors: Saira Bhatti; M. A. Rana, A. M. Siddiqui, M. Zahid, Hafiz Abdul Wahab.Computational Ecology Software,2016,6(3):106-119
Abstract: This paper presents the analysis of the process of blade coating through a computational intensive method for an incompressible Newtonian fluid along with Magnetohydrodynamics (MHD). The slip between the substrate and the fluid is also taken into account. The nature of the existing steady solutions has been investigated with the help of exact and numerical methods. Those obtained exact solutions include the solutions for the velocity profiles, volumetric flow rate and pressure gradient. The important engineering quantities like maximum pressure, pressure distribution and load are also computed. It is assumed that the relative velocity between the plate and the fluid is proportional to the shear rate at the plate. An external magnetic field is applied normal to the plates. It is observed and concluded that both slip parameter and the magnetic field parameter serve as the controlling parameters in the industrial blade coating process.
- Network toxicology: A new science
Authors: WenJun Zhang.Computational Ecology; Software,2016,6(2):31-40
Abstract: Network toxicology is related to network biology. Based on my previous study (Zhang, 2016c), in present article I further outlined and defined the aims, scope, theory and methodology of network toxicology.
- The exact solutions of nonlinear problems by Homotopy Analysis Method
(HAM)
Authors: Hafiz Abdul Wahab; Saira Bhatti, Mohammad Naeem.Computational Ecology Software,2016,6(2):41-54
Abstract: The present paper presents the comparison of analytical techniques. We establish the existence of the phenomena of the noise terms in the perturbation series solution and find the exact solution of the nonlinear problems. If the noise terms exist, the Homotopy Analysis method gives the same series solution as in Adomian Decomposition Method as well as homotopy Perturbation Method (Wahab et al, 2015) and we get the exact solution using the initial guess in Homotopy Analysis Method using the results obtained by Adomian Decomposition Method.
- Fluctuating asymmetry in evaluating the developmental instability of
Glossogobius giuris (Hamilton, 1822) from Lake Mainit, Surigao del Norte,
Philippines
Authors: C.C.D.Joseph; J.H. Jumawan, B.J. Hernando, L.Z. Boyles, J.C. Jumawan, J.P.B.Velasco, C.C.Cabuga, S.O.M.A. Abastillas, E.A. Requieron, M.A.J. Torres.Computational Ecology Software,2016,6(2):55-65
Abstract: This study was conducted to assess the status of Lake Mainit by using fluctuating asymmetry in the populations of Glosogobius giuris. A total of 200 G. giuris was collected with 100 per sex. All the samples were placed in a flat styrofoam for the pinning of its fins to make it wider and to clearly see the samples point of origin for the land-marking process. 10% Formalin was applied in all the fins of the fish samples to make it hardened using a small brush. Twenty (20) landmarks were used to analyze the body shape of the fish. Several studies proved that FA can be used to directly assess water quality and the overall status of the ecosystem. Using thin-plate spline (TPS) series, landmark analyses were obtained and subjected to Symmetry and Asymmetry in Geometric Data (SAGE) software. Results in Procrustes ANOVA showed that individual symmetry showed a highly significant difference (P = 0.00) as well as Sides (Directional Asymmetry) and Interaction (Fluctuating Asymmetry) in the study area. All the samples showed FA in both sexes. The results of Principal Component Scores displayed a higher percentage in female (69.2797%) than male (63.9214%) from Lake Mainit. Variations are almost found in all the body part of the goby in female and male gobies except for anterior insertion of second dorsal fin and superior margin of the preoperculum. Females have a higher fluctuating asymmetry than in males. Females spawn and males protect the eggs from any predators. In this case, females are more susceptible to stress because they have to forage in order to compensate the energy used up during spawning. Males are less susceptible because they usually stay on the nesting ground, and don't have to cover far distances in finding food. This study validates the use of FA in determining the status of the fishes caught connecting to what the status of the environment is based on the result.
- Evaluating the developmental instability of Scatophagus argus (Linnaeus,
1766) from Lower Agusan River Basin, Butuan City, Philippines using
fluctuating asymmetry
Authors: J.H. Jumawan; J.P.B. Velasco, A.O. Mondejar, M.B. Madelozo, L.M.C. Segovia, K.C.T. Necesito, J.R.U. Licayan, J.C. Jumawan, M.A.J. Torres, E.A. Requieron.Computational Ecology Software,2016,6(1):1-11
Abstract: Fluctuating Asymmetry (FA) is the most frequently used tool for measuring developmental instability. It is used as a measure of ecological stress and a sign of developmental stability of organisms. The study evaluatedthe use of FA in assessing the condition of Scatophagus argus in lower Agusan river basin. High FA values would indicate exposure to polluted aquatic environment. The study selected S. argus because of its observed susceptibility to aquatic pollution in the area. There were a total of 60 samples collected (30 males and 30 females). Using Thin-Plate Spline (TPS) series, landmark analyzes were obtained and subjected to Symmetry and Asymmetry in Geometric Data (SAGE) software. Procrustes ANOVA showed high significant differences (P less than 0.0001) to the three measured factors (individuals, sides and interaction of individuals and sides). Similar findings were observed to both male and females samples suggesting high FA values. The principal component analysis was implemented to determine the affected landmarks. More landmarks were affected in males (11 landmarks) than in females (5 landmarks). Deformation grids and histograms were used to display the ordination of affected landmarks. The data would be important to environmental planners in the management of lower Agusan river basin. Scores display a high percentage FA of female (70.94%) and male (78.67%). In the female samples, PC 1 (33.26%) and PC2 (13.53%) were found to have significant variations affecting the rostral tip of premaxilla, posterior extremities, and the lateral profile. In the male samples, PC 1 (35.63%) and PC 2 (14.24%) have the same affected landmarks as in females but have greater variations. Significant levels of FA in the fish morphology are the result of its adaptive mechanism to cope up with the stressed environment. The dorsal cephalic region and the pectoral fin were the most affected landmarks and may be used to determine the effect of stressors to the fish since these areas were involved in fish mobility. Thus, the high FA in the body shapes of spotted scat suggests that ecological health in the area is in not good standing.
- Calculating the uncertainty associated to the forecast of species
dispersals: Stochastic Flow Connectivity
Authors: Alessandro Ferrarini.Computational Ecology; Software,2016,6(1):12-20
Abstract: To date, corridors for species dispersals have been thought as deterministic outputs emerging from some kind of model. Uncertainty about the individuation of biotic corridors has never been considered. Flow connectivity (FC) is a methodology first introduced in 2013 to forecast biotic flows over real landscapes, alternative to both circuit theory and least-cost modelling. Its name is due to the fact that it resembles in some way the motion characteristic of fluids over a surface. FC predicts species dispersal by minimizing at each time step the potential energy due to fictional gravity force over a frictional 3D landscape built upon the real landscape. In this work, FC is further developed to find a solution to the problem of calculating the uncertainty associated to the forecast of species dispersals. The output of this method is an ''uncertainty polygon'' (e.g., 5% or 10% uncertainty) around the predicted biotic flow. The importance of this new variant of FC is clear: when planning greenways for biodiversity, uncertainty about biotic flows prediction must be taken into account and the planned corridors must encompass the ''uncertainty polygon'' as well, otherwise they are at serious risk to underestimate the necessary space required by animal species to flow over landscape.
- Coral reef assessment and monitoring made easy using Coral Point Count
with Excel extensions (CPCe) software in Calangahan, Lugait, Misamis
Oriental, Philippines
Authors: S. R. M. Tabugo; D.L. Manzanares, A.D. Malawani.Computational Ecology Software,2016,6(1):21-30
Abstract: Coral reef communities are considered as the most diverse marine ecosystems that provide food, shelter and protection to marine organisms. It provides many important benefits to humans but often a subject to impairment through human activities. Cascading human influences and climate change appeared as a reason behind its decline. Thus, coral reef monitoring methods are substantial. This study utilized Coral Point Count with Excel extensions (CPCe) software, as a means to increase efficiency of coral reef monitoring efforts because it automates, facilitates and speeds the process of random point count analysis and can perform image calibration, planar area and length calculations of benthic features. The method was used to estimate community statistics of benthos based on captured still images for every 1m marked across four 50m transect line (total 200 m) at 4.6-5.6m depth. Transect images were assigned with 30 spatial random points for identification. Multiple image frames were combined for each transect length supplying datasheet containing header information, statistical parameters species or substrate type (relative abundance, mean and standard deviation) and Shannon-Weaver and Simpson's Index calculation for species diversity. Generated transect datasets were statistically analyzed to give quantitative population estimates over the area of interest. Data from individual frames were combined per transect to allow both inter- and intra- site/transect comparisons. This study reports the current status of coral reefs across Calangahan, Lugait, Misamis Oriental, Philippines and proved the efficiency of CPCe as a tool in reef assessment and monitoring. Results showed that most common genera Porites and Acropora were dominant, with Porites lobata as the most abundant coral species in the area. Moreover, results also showed that there were various diseases present affecting corals leading to increased mortality.
- Pattern recognition and simulation in ecology
Authors: Xiaozhuo Han; Meng Gao, Cang Hui.Computational Ecology Software,2015,5(4):271-275
Abstract: In ecology, the patterns usually refer to all kinds of nonrandom spatial and temporal structures of ecosystems driving by multiple ecological processes. Pattern recognition is an important step to reveal the complicated relationship between ecological patterns and processes. To review and present some advances about ecological modeling, patterns recognition, and computer simulation, an international workshop on Mathematical and Numerical Ecology with the theme "Pattern recognition and simulation in ecology" was held in in October 2014 in Guangzhou, China, and the International Society of Computational Ecology was the co-sponsor. Eight peer-reviewed papers those were originally presented at this workshop covering three themes: patterns in phylogeny, patterns in communities and ecosystems, and spatial pattern analysis are included in this special issue.
- Particle swarm optimization algorithm for parameter estimation in
Gamma-Poisson distribution model of k-tree distance
Authors: Feixia Lu; Dingyuan Mo, Meng Gao.Computational Ecology Software,2015,5(4):276-285
Abstract: Distance sampling is a flexible and efficient inventory technique in forestry and ecology, especially in highly dense plant communities, and in difficult terrain. Point-to-tree distance or tree-to-tree distance was used to estimate characteristics of the spatial point pattern mapped from particular spatial locations of plant or tree individuals. For random spatial point patterns, there is an ideal probability distribution model of point-to-tree distance resulting in unbiased density estimators. For aggregated spatial point patterns, Gamma-Poisson probability model of point-to-tree distance corresponding to Gamma-Poisson point process is one candidate model. Although the density estimator based on Gamma-Poisson model is biased, it performs satisfactorily in practical applications. However, numerical method to compute the maximum likelihood estimates of Gamma-Poisson model is very complicated. In this paper, a parameter optimization method, particle swarm optimization algorithm, is applied for parameter estimation in Gamma-Poisson model. The results showed that the new parameter estimation method was efficient and not constrained by the sample size; therefore, the computational complexity was significantly reduced. We suggest this parameter optimization for density estimation in forestry and ecology.
- Spatial distributions of niche-constructing populations
Authors: Xiaozhuo Han; Yaling Huang, Cang Hui.Computational Ecology Software,2015,5(4):286-298
Abstract: Niche construction theory regards organisms not only as the object of natural selection but also an active subject that can change their own selective pressure through eco-evolutionary feedbacks. Through reviewing the existing works on the theoretical models of niche construction, here we present the progress made on how niche construction influences genetic structure of spatially structured populations and the spatial-temporal dynamics of metapopulations, with special focuses on mathematical models and simulation methods. The majority of results confirmed that niche construction can significantly alter the evolutionary trajectories of structured populations. Organism-environmental interactions induced by niche construction can have profound influence on the dynamics, competition and diversity of metapopulations. It can affect fine-scale spatially distribution of species and spatial heterogeneity of the environment. We further propose a few research directions with potentials, such as applying adaptive dynamics or spatial game theory to explore the effect of niche construction on phenotypic evolution and diversification.
- Effect of spatial structure on the evolution of cooperation based on game
models
Authors: Hui Zhang; Meng Gao.Computational Ecology Software,2015,5(4):299-316
Abstract: To elucidate the mechanisms for the evolution of cooperation has been a core problem in biology, economics and sociology. Evolutionary game theory has proven to be an efficient approach to investigate the problem by using models based on so-called social dilemmas. Spatial structure is indicated to have an important effect on the evolution of cooperation and has been intensively studied during recent years. From this perspective, we review our studies in evolutionary dynamics based on a repeated game with three strategies, 'always defect' (ALLD), 'tit-for-tat' (TFT), and 'always cooperate' (ALLC). With mathematical analysis and numerical simulations, the results show that cooperation can be promoted in spatially-structured populations. Cooperators prevail against defectors by forming stable clusters, which is called the `spatial selection'. Meanwhile, lattice structure also inhibits cooperation due to the advantage of being spiteful. Furthermore, simulations demonstrate that a slight enforcement of ALLC can only promote cooperation when there is weak network reciprocity, while the catalyst effect of TFT on cooperation is verified.
- The architecture of antagonistic networks: Node degree distribution,
compartmentalization and nestedness
Authors: Savannah Nuwagaba; Cang Hui.Computational Ecology Software,2015,5(4):317-327
Abstract: Describing complex ecosystems as networks of interacting components has proved fruitful - revealing many distinctive patterns and dynamics of ecological systems. Of these patterns, three have often been brought up in literature, including species degree distribution, compartmentalization and nestedness, due largely to their implications for the functionality and stability of communities. Here, using 61 empirical antagonistic networks, we aim to settle the inconsistency in literature by (i) fitting their node degree distributions to five different parametric models and identifying the one fits the best, (ii) measuring the levels of nestedness and compartmentalization of these 61 networks and testing their significance using different null models, and (iii) exploring how network connectance affects these three network architecture metrics. This research showed that most antagonistic networks do not display power law degree distributions and that resource species are generally uniformly distributed. We also clearly showed that the conclusion of whether a network is significantly compartmentalized or nested depends largely on the null model used.
- An introduction to phylogenetic analyses and modelling in ecology
Authors: H.O. Minoarivelo; G. Diedericks, C. Hui.Computational Ecology Software,2015,5(4):328-339
Abstract: Phylogenetic systematics seeks to describe and reconstruct the evolutionary relationships among and between organisms making use of molecular data. This field has become immensely popular in recent years, with the associated computational demands growing in leaps and bounds. Here, we review the progress made in statistical phylogenetics, compare the various methods and highlight the recent trends and pitfalls. Furthermore, we delve into the mathematical models associated with these methods to understand the underlying assumptions, while tracking the improvements made. Lastly, we look at the impact and use of phylogenetics in ecology.
- Forms and genesis of species abundance distributions
Authors: Evans O. Ochiaga; Cang Hui.Computational Ecology Software,2015,5(4):340-353
Abstract: Species abundance distribution (SAD) is one of the most important metrics in community ecology. SAD curves take a hollow or hyperbolic shape in a histogram plot with many rare species and only a few common species. In general, the shape of SAD is largely log-normally distributed, although the mechanism behind this particular SAD shape still remains elusive. Here, we aim to review four major parametric forms of SAD and three contending mechanisms that could potentially explain this highly skewed form of SAD. The parametric forms reviewed here include log series, negative binomial, lognormal and geometric distributions. The mechanisms reviewed here include the maximum entropy theory of ecology, neutral theory and the theory of proportionate effect.
- Modelling spread with context-based dispersal strategies
Authors: Andriamihaja Ramanantoanina; Cang Hui.Computational Ecology Software,2015,5(4):354-366
Abstract: Dispersal is a context-dependent adaptive trait. Different dispersal strategies arise as species need to optimize their fitness in the ever changing quality of habitats further imposed by abiotic and biotic factors. This work reviews the spread of populations under different dispersal strategies. Namely, we address the spread of a population when dispersal is driven by habitat fragmentations, density-dependent predation and mixed propagules. The context-based dispersal can explain a variety of range dynamics. It is of common accord however that the cause and effect of dispersal could have a wider effect on population dynamics that goes beyond purely ecological nature.
- Modeling at the Interface of ecology and epidemiology
Authors: Min Su; Hong Wang.Computational Ecology Software,2015,5(4):367-379
Abstract: We briefly present a synthesis of theoretical models in eco-epidemiology which merges the fields of ecology and epidemics. In particular we discuss the role of parasites/pathogens in community assembly formation and species coexistence, as well as the potential of biological control. Recent works have revealed that the complexity in parasite-mediated interactions can alter the dynamic behavior of eco-epidemiological systems, exhibiting oscillations, switching stability regimes. Both community structure and interaction strength also can affect the role of parasites in the host-parasite dynamics. The emerging research area focuses on the spatial structure and distribution pattern in eco-epidemiology. Compared with the well mixed system, spatial structure in eco-epidemiology can lead to different dynamic behavior. We therefore highlight the need to address the impact of parasites/pathogens on real community structures and combine the evolutionary potential to predict the complex dynamics during the biological control in eco-epidemiological systems.
- A discrete homotopy perturbation method for non-linear Schrodinger
equation
Authors: H. A. Wahab; Khalid Usman, Muhammad Naeem, Sarfraz Ahmad, Saira Bhatti, Muhammad Shahzad, Hazrat Ali.Computational Ecology Software,2015,5(4):380-388
Abstract: A general analysis is made by homotopy perturbation method while taking the advantages of the initial guess, appearance of the embedding parameter, different choices of the linear operator to the approximated solution to the non-linear Schrodinger equation. We are not dependent upon the Adomian polynomials and find the linear forms of the components without these calculations. The discretised forms of the nonlinear Schrodinger equation allow us whether to apply any numerical technique on the discritisation forms or proceed for perturbation solution of the problem. The discretised forms obtained by constructed homotopy provide the linear parts of the components of the solution series and hence a new discretised form is obtained. The general discretised form for the NLSE allows us to choose any initial guess and the solution in the closed form.
- Method of extreme points: Characteristics of feasible sets for forecast of
population dynamics
Authors: L.V. Nedorezov.Computational Ecology; Software,2015,5(4):389-401
Abstract: In current publication within the framework of method of extreme points various characteristics of feasible sets are applied for forecast of population dynamics. Following characteristics were used: maximum, minimum and average values for all trajectories with parameters belonging to feasible set, trajectory with best characteristics for Kolmogorov - Smirnov criterion, and trajectory with lowest value of sum of squared deviations between theoretical and empirical values. Analyses were provided for larch bud moth population (Zeiraphera diniana Gn.) time series (GPDD 1407; sample size is 38) and for Moran - Ricker model. Time series was divided onto two parts: for first part (first 21 values or more) feasible sets were determined and for tails of time series pointed out characteristics were applied. Forecasting properties of used characteristics are under discussion.
- Bifurcation and complex dynamics of a discrete-time predator-prey system
involving group defense
Authors: S. M. Sohel Rana.Computational Ecology; Software,2015,5(3):222-238
Abstract: In this paper, we investigate the dynamics of a discrete-time predator-prey system involving group defense. The existence and local stability of positive fixed point of the discrete dynamical system is analyzed algebraically. It is shown that the system undergoes a flip bifurcation and a Neimark-Sacker bifurcation in the interior of R+2 by using bifurcation theory. Numerical simulation results not only show the consistence with the theoretical analysis but also display the new and interesting dynamical behaviors, including phase portraits, period-7, 20-orbits, attracting invariant circle, cascade of period-doubling bifurcation from period-20 leading to chaos, quasi-periodic orbits, and sudden disappearance of the chaotic dynamics and attracting chaotic set. The Lyapunov exponents are numerically computed to characterize the complexity of the dynamical behaviors.
- Impact of environmental factors on maintaining water quality of Bakreswar
reservoir, India
Authors: Moitreyee Banerjee; Joyita Mukherjee, Arnab Banerjee, Madhumita Roy, Goutam Bandyopdhyay, Santanu Ray.Computational Ecology Software,2015,5(3):239-253
Abstract: Reservoirs and dams are engineered systems designed to serve purposes like supply of drinking water as well as other commercial and industrial use. A thorough assessment of water quality for these systems is thus necessary. The present study is carried out at Bakreswar reservoir, in Birbhum district, which was created by the dam, built on Bakreswar River. The major purpose of the reservoir is the supply of drinking water to the surrounding villages and Bakreswar Thermal Power Station. Water samples were collected fortnightly from three different stations of the reservoir. Physical and chemical factors like dissolved oxygen, atmospheric temperature, pH, conductivity, salinity, solar radiation, water temperature, alkalinity, hardness, chloride, productivity etc. were analysed using standard procedure. Abundance data is calculated for four major groups of zooplanktons (Cladocera, Copepoda, Ostracoda, and Rotifera) with the software PAST 2.1. Multivariate statistical analysis like PCA, hierarchical cluster and CCA are performed in order to predict the temporal variation in the water quality factors using SPSS 20. Distinct seasonal variation was found for environmental factors and zooplankton groups. Bakreswar reservoir has good assemblage of zooplankton and distinct temporal variation of environmental factors and its association with zooplankton predicts water quality condition. These results could help in formulating proper strategies for advanced water quality management and conservation of reservoir ecosystem. Key elements for growth and sustenance of the system can then be evaluated and this knowledge can be further applied for management purposes.
- Measuring the complex behavior of the SO2 oxidation reaction
Authors: Muhammad Shahzad; Sumaira Rehman, Rabia Bibi, Hafiz Abdul Wahab, Saleem Abdullah, Sarfraz Ahmed.Computational Ecology Software,2015,5(3):254-270
Abstract: The two step reversible chemical reaction involving five chemical species is investigated. The quasi equilibrium manifold (QEM) and spectral quasi equilibrium manifold (SQEM) are used for initial approximation to simplify the mechanisms, which we want to utilize in order to investigate the behavior of the desired species. They show a meaningful picture, but for maximum clarity, the investigation method of invariant grid (MIG) is employed. These methods simplify the complex chemical kinetics and deduce low dimensional manifold (LDM) from the high dimensional mechanism. The coverage of the species near equilibrium point is investigated and then we shall discuss moving along the equilibrium of ODEs. The steady state behavior is observed and the Lyapunov function is utilized to study the stability of ODEs. Graphical results are used to describe the physical aspects of measurements.
- Fluctuating asymmetry and developmental instability in Protoreaster
Authors: D.J. V. Trono; R. Dacar, L. Quinones, S. R. M. Tabugo.Computational Ecology Software,2015,5(2):119-129
Abstract: Fluctuating asymmetry (FA), pertains to small and random departures from perfect symmetry of an organism's bilateral traits and has been used as a measurement of developmental instability and as a potential indicator of stress in populations. It measures the variations from symmetry of a symmetrical structure whose sides are said to be genetically identical, with similar history of gene activity and experiencing the same environment. Symmetries are potentially the basis for studies on FA. Hence, this study assessed the potential of FA as a reliable developmental instability and environmental stress indicator in five-fold dihedral symmetrical Protoreaster nodosus (Chocolate chip sea fish) from three (3) different sites (Linamon, Lanao del Norte; Initao, Misamis Oriental and Jasaan, Misamis Oriental). FA for each population from every site was measured for comparison. In this study, anatomical landmarks were subjected to Procrustes superimposition and Principal Component Analysis (PCA) using "Symmetry and Asymmetry in Geometric Data" (SAGE) program. Results showed highly significant FA and significant DA for population from Jasaan and Linamon where habitat disturbance due to anthropogenic activities were prevalent. Thus, experienced more stress compared to the other populations, suggesting that significant variation in size or left-right side of each individual could be a product of genotype-environment interaction. Moreover, insignificant FA and high DA was obtained from Initao (protected seascape area) which indicated that variation among individual genotypes and asymmetry in phenotypes is mostly induced by genetics under less stressful environment. Significant FA and increase FA present inability of species to buffer stress in its developmental pathways and have implications on species fitness. Hypothesis assumes that fluctuating asymmetry has costs, reflects the quality of individuals and the level of genetic and environmental stress experienced by individuals or populations during development. Here, FA proved to be efficient when applied to five-fold dihedral symmetrical organisms.
- Distinguishing niche and neutral processes: Issues in variation
partitioning statistical methods and further perspectives
Authors: Youhua Chen.Computational Ecology; Software,2015,5(2):130-138
Abstract: Variance partitioning methods, which are built upon multivariate statistics, have been widely applied in different taxa and habitats in community ecology. Here, I performed a literature review on the development and application of the methods, and then discussed the limitation of available methods and the difficulties involved in sampling schemes. The central goal of the work is then to propose some potential practical methods that might help to overcome different issues of traditional least-square-based regression modeling. A variety of regression models has been considered for comparison. In initial simulations, I identified that generalized additive model (GAM) has the highest accuracy to predict variation components. Therefore, I argued that other advanced regression techniques, including the GAM and related models, could be utilized in variation partitioning for better quantifying the aggregation scenarios of species distribution.
- Application of homotopy perturbation method to the Navier-Stokes equations
in cylindrical coordinates
Authors: H. A. Wahab; Anwar Jamal, Saira Bhatti, Muhammad Naeem, Muhammad Shahzad, Sajjad Hussain.Computational Ecology Software,2015,5(2):139-151
Abstract: This paper deals with the approximate analytical solution of the Navier-Stokes equations in cylindrical coordinates. The homotopy perturbation method is used to get the analytical approximation. Depending upon different available choices for the linear operator, we also have the advantage to choose different initial approximations to start our analysis. The analysis is done without calculating the Adomian's polynomials.
- Modeling the effect of pollution on biological species: A socio-ecological
problem
Authors: B. Dubey; J. Hussain, S. N. Raw, Ranjit Kumar Upadhyay.Computational Ecology Software,2015,5(2):152-174
Abstract: In this paper, a nonlinear spatial model is proposed and analyzed to study the effect of pollution on biological population. It is assumed that the pollutants enter into the environment not directly by the population but by a precursor produced by the population itself. It is further assumed that larger the population, faster the precursor is produced, and larger the precursor, faster the pollutant is produced. Criteria for nonlinear stability and instability for both spatial and non-spatial models are obtained. The various parameter ranges for stable homogeneous solutions are identified. By the simulation experiments, it is observed that by applying an appropriate effort F , the population density P can be maintained at a higher equilibrium level. It is also shown that the equilibrium level of the concentration of precursor pollutant, concentration of pollutant in the environment and in the population decrease due to the effort F.
- Hopf bifurcation and stability analysis for a delayed logistic equation
with additive Allee effect
Authors: E.M. Elabbasy; Waleed A.I. Elmorsi.Computational Ecology Software,2015,5(2):175-186
Abstract: In this paper the linear stability of the delayed logistic equation with additive Allee effect is investigated. We also analyze the associated characteristic transcendental equation, to show the occurrence of Hopf bifurcation at the positive equilibrium. To determine the direction of Hopf bifurcation and the stability of bifurcating periodic solution, we use the normal form approach and a center manifold theorem. Finally, a numerical example is given to demonstrate the effectiveness of the theoretical analysis.
- Bifurcation and complex dynamics of a discrete-time predator-prey
system
Authors: S. M. Sohel Rana.Computational Ecology; Software,2015,5(2):187-200
Abstract: In this paper, we investigate the dynamics of a discrete-time predator-prey system of Holling-I type in the closed first quadrant R+ square. The existence and local stability of positive fixed point of the discrete dynamical system is analyzed algebraically. It is shown that the system undergoes a flip bifurcation and a Neimark-Sacker bifurcation in the interior of R+ square by using bifurcation theory. It has been found that the dynamical behavior of the model is very sensitive to the parameter values and the initial conditions. Numerical simulation results not only show the consistence with the theoretical analysis but also display the new and interesting dynamic behaviors, including phase portraits, period-9, 10, 20-orbits, attracting invariant circle, cascade of period-doubling bifurcation from period-20 leading to chaos, quasi-periodic orbits, and sudden disappearance of the chaotic dynamics and attracting chaotic set. In particular, we observe that when the prey is in chaotic dynamic, the predator can tend to extinction or to a stable equilibrium. The Lyapunov exponents are numerically computed to characterize the complexity of the dynamical behaviors. The analysis and results in this paper are interesting in mathematics and biology.
- Modeling and analysis of the survival of a biological species in a
polluted environment: Effect of environmental tax
Authors: Shyam Sundar; Ram Naresh.Computational Ecology Software,2015,5(2):201-221
Abstract: In this paper, a nonlinear dynamical model is proposed and analyzed to study the survival of biological species in a polluted environment considering the effect of environmental tax which can be used further to improve environmental quality. The environmental tax is imposed to control the emission of pollutants/toxicants only when the equilibrium concentration of pollutants go beyond its threshold level causing harm to the biological species and its ecosystem under consideration. Local and nonlinear stability conditions are obtained by considering suitable Liapunov function. Numerical simulation of the dynamical system is performed in order to illustrate the analytical findings. It is shown that the density of biological species decreases as the concentration of pollutants increases and may even become extinct if the concentration is very high. It has also been shown that the environmental tax plays an important role to control the concentration of pollutants in the atmosphere and maintaining the density of biological species at a desired level.
- Generating and prioritizing optimal paths using ant colony
optimization
Authors: Mukesh Mann; Om Prakash Sangwan.Computational Ecology Software,2015,5(1):1-15
Abstract: The assurance of software reliability partially depends on testing. Numbers of approaches for software testing are available with their proclaimed advantages and limitations, but accessibility of any one of them is a subject dependent. Time is a critical factor in deciding cost of any project. A deep insight has shown that executing test cases are time consuming and tedious activity. Thus stress has been given to develop algorithms which can suggest better pathways for testing. One such algorithm called Path Prioritization -Ant Colony Optimization (PP-ACO) has been suggested in this paper which is inspired by real Ant's foraging behavior to generate optimal paths sequence of a decision to decision (DD) path of a graph. The algorithm does full path coverage and suggests the best optimal sequences of path in path testing and prioritizes them according to path strength.
- Turing and Non-Turing patterns in diffusive plankton model
Authors: N. K. Thakur; R. Gupta, R. K. Upadhyay.Computational Ecology Software,2015,5(1):16-27
Abstract: In this paper, we investigate a Rosenzweig-McAurthur model and its variant for phytoplankton, zooplankton and fish population dynamics with Holling type II and III functional responses. We present the theoretical analysis of processes of pattern formation that involves organism distribution and their interaction of spatiallydistributed population with local diffusion. The choice of parameter values is important to study the effect of diffusion, also it depends more on the nonlinearity of the system. With the help of numerical simulations, we observe the formation of spatiotemporal patterns both inside and outside the Turing space.
- Chaotic dynamics in a discrete-time predator-prey food chain
Authors: S. M. Sohel Rana.Computational Ecology; Software,2015,5(1):28-47
Abstract: In this paper, we consider a classical discrete-time food chain model describing predators-prey interaction. The Holling type I functional response is used as the uptake for both predators. The existence and local stability of fixed points of the discrete dynamical system are analyzed algebraically. Using growth rate of prey as the bifurcation parameter, it is shown that the system undergoes a flip and Hopf bifurcations around planer or interior fixed point. It has been found that the dynamical behavior of the model is very sensitive to the parameter values and the initial conditions. Numerical simulations not only illustrate the key points of analytical findings but also exhibit complex dynamical behaviors of the model, such as the phase portraits, cascade of period-doubling bifurcation and determine the effects of operating parameters of the model on its dynamics. The Lyapunov exponents are numerically computed to characterize the asymptotic stability of the system dynamic response and estimate the amount of chaos in the system.
- Local stability of an open-access anchovy fishery model
Authors: M. N. Qureshi; A. Q. Khan.Computational Ecology Software,2015,5(1):48-62
Abstract: In this paper, we study the qualitative behavior of following open-access anchovy fishery model: xn+1=axnb-dalphaxvnyn, yn+1=yn(hpalphaxvn-c)+1), where a,b,c,d,v,p,alpha,h and the initial conditions x0, y0 are positive real numbers. More precisely, we investigate the necessary and sufficient condition for local asymptotic stability of the unique positive equilibrium point of this system. Some numerical examples are given to verify our theoretical results.
- Incorporating climatic change into ecological connectivity: Climatic Flow
Connectivity
Authors: Alessandro Ferrarini.Computational Ecology; Software,2015,5(1):63-68
Abstract: There's an urgent need of theoretical and methodological tools to predict how much and how climate change will impact animal movements. In fact, conservation planning aimed to facilitate species movement in the face of climate change strictly requires realistic predictions of where species will likely move to reach suitable climates, and through which suitable routes such biotic shifts will happen. Climatic Flow Connectivity is introduced here with such purpose. Climatic Flow Connectivity calculates the spatial divergence due to climate change of the biotic flow with respect to the inertial biotic flow (i.e. where no climate change is considered) over landscape. So doing, Climatic Flow Connectivity not only predicts the most likely biotic routes imposed by climatic change to one species, but also estimates the impact of climate change in terms of spatial divergence and differential shift effort with respect to the inertial (no climate change) scenario. Climatic Flow Connectivity takes advantage of the previously introduced Flow Connectivity, and it comes with the software Connectivity Lab whose outputs are the vectors of the faunal (inertial and climatic) movement plus the statistics of the movement (inertial and climatic) efforts.
- Towards cardinality-based service feature diagrams
Authors: Ghulam Mustafa Assad; Muhammad Naeem, Hafiz Abdul Wahab.Computational Ecology Software,2015,5(1):69-76
Abstract: To provide efficient services to end-user it is essential to manage variability among services. Feature modelling is an important approach to manage variability and commonalities of a system in product line. Feature models are composed of feature diagrams. Service feature diagrams (an extended form of feature diagrams) changed the basic framework of feature diagrams by proposing new feature types and their relevance. Service feature diagrams provide selection rights for variable features. In this paper we argue that it is essential to put cardinalities on service feature diagrams. That is, the selection of features should be done under some constraints, to provide a lower and upper limit for the selection of features. The use of cardinalities on service feature diagrams reduces the types of features to half, while keeping the integrity of all features.
- Semantics of the maturity model for feature oriented domain analysis
Authors: M. Javed; M. Naeem, H. A. Wahab.Computational Ecology Software,2015,5(1):77-112
Abstract: Assessing the quality of a model has always been a challenge for researchers in academia and industry. The quality of a feature model is a prime factor in software development because it is used in the development of products. This paper elaborates on our previous work where, we have motivated the need of the maturity model along with the description of such model for feature oriented domain analysis. Here, we provide the semantics of such maturity model. Furthermore, in this extended version, we present an algorithmic technique for the detection of quality level for a given feature model.
- Impact of Open Source software on the environmental protection
Authors: D. Viduka; A. Basic.Computational Ecology Software,2015,5(1):113-118
Abstract: Ongoing development of computer hardware contributes to the constant throwing old computers ie. direct increase of electric and electronic equipment waste. This type of waste is a major threat to human health and the environment. By applying Open Source software solutions all users of computer hardware can significantly effect on the reduction of this type of waste. The aim of this paper is to present the advantages of using Open Source software package in terms of preserving and protecting the environment. This paper presents the results of testing MS Windows and Linux operating systems on an older computer, the results are obtained by applying the benchmark software GeekBench.
- Siplab, a spatial individual-based plant modelling system
Authors: Oscar Garcia.Computational Ecology; Software,2014,4(4):215-222
Abstract: Spatially-explicit individual-based models are important tools in forestry and plant ecology. They are commonly implemented through custom computer coding that is time-consuming, may cause compatibility and availability problems, and makes difficult the evaluation, comparison and re-use of model components. Siplab is an R package that aims at improving this situation with a flexible computing environment that can handle a variety of model forms, and without requiring advanced programming knowledge. The article briefly reviews spatial individual-plant models, and then explains the general framework used by siplab to represent such models in a unified way. The structure and practical use of the package are introduced through some of the examples previously discussed.
- Ecological connectivity: Flow connectivity vs. least cost modelling
Authors: Alessandro Ferrarini.Computational Ecology; Software,2014,4(4):223-233
Abstract: Recently I have introduced a modelling approach (flow connectivity) to ecological connectivity that is alternative to circuit theory, and is able to fix the weak point of the "from-to" connectivity approach. Flow connectivity also holds for mountain and hilly landscapes that are not composed of source and sink habitats. In this paper I compare the recently-introduced flow connectivity (FC) modelling to the commonly-used least cost (LC) modelling. LC path analysis is an attractive technique for analysing and designing habitat corridors because it: 1) allows quantitative comparisons of potential movement routes over large study areas, 2) can incorporate simple or complex models of habitat effects on movement and 3) offers the potential to escape the limitations of analyses based solely on structural connectivity (i.e. designating areas as patch, matrix or corridor) by modelling connectivity as it might be perceived by a species on a landscape. I evidence here that flow connectivity has the same advantages when compared to LC modelling as with regard to circuit theory. Four main differences emerged. LC modelling a) is a "from-to" approach to ecological connectivity, b) it seeks global path optimization, c) it allows for biotic paths where the biotic effort is ascending, and d) it is undirected (it does not depend on the direction of the path). FC has opposite properties. Moreover, costdistance models are based on two biologically improbable assumptions: (1) dispersers have complete knowledge of their surroundings, and (2) they do select the least cost route from this information. Instead, the predicted path lengths and the biotic efforts predicted by both FC and LC modelling in a case study about wolf in the Ceno valley (Parma, Italy) resulted not significantly different, but this result is contingent upon the case study.
- About a model of biological population data collection: Can
heteroscedasticity problem be solved or not?
Authors: L. V. Nedorezov.Computational Ecology; Software,2014,4(4):234-247
Abstract: In paper stochastic model with discrete time of migrations in finite part of plane is considered. It is assumed that migrations can be from every node of integer lattice to nearest nodes only, and these migrations depend on numbers of individuals in the respective nodes. Population size is assumed to be constant for every sequence of population size measurements. It is also assumed that there are two limits D1 and D2, D1, D1 less than D2, of local population size in node when respective node is attractable for migrants (Alley effect). If local population size is bigger than D2 node becomes unsuitable for migrants, and all individuals try to leave the respective node. After a certain number of time steps local population size is determined in randomly selected nodes (it looks like method of "throwing of frame" or "cutting of model trees" of entomological data collection but in considering situation it doesn't lead to changing of conditions for population). Dependence of standard deviations of samples of various sizes on fixed values of population density are analyzed. In particular, it is shown that well-known problem of heteroscedasticity cannot be solved in principle for the situation when ecological model parameters must be estimated using empirical or experimental time series. Analysis of dependence of number of interactions of individuals per time step (average in time and space) on total population size allows pointing out new ways in modification of Verhulst model.
- Modeling the dynamics of carbon dioxide removal in the atmosphere
Authors: Shyam Sundar; Ram Naresh, Ashish Kumar Mishra, Agraj Tripathi.Computational Ecology Software,2014,4(4):248-268
Abstract: The temperature of Earth's surface is increasing over the past few years due to emission of global warming gases such as CO2, CH4 and NOx from industries, power plants, etc., leading to several adverse effects on human and his environment. Therefore, the question of their removal/reduction from the atmosphere is very important. In this paper, a nonlinear mathematical model to study the removal/reduction of carbon dioxide by using suitable absorbent (such as aqueous ammonia solution, amines, sodium hydroxide, etc.) near the source of emission and externally introducing liquid species in the atmosphere is presented. Dynamical properties of the model which include local and global stabilities for the equilibrium are analyzed carefully. Model analysis is performed by considering three physical situations i.e. when both absorbent and the liquid species are used, only absorbent is used and only liquid species is used. It is shown that the concentration of carbon dioxide decreases as the rate of introduction of absorbent in the absorber increases. It decreases further as the rate of introduction of liquid species. Thus, the concentration of carbon dioxide would be reduced by a large amount if adequate amount of absorbent is used near the source of emission. The remaining amount can be reduced further by infusing liquid drops in the atmosphere. Numerical simulations are also carried out to support the analytical results.
- Estimate of soil organic carbon and greenhouse gas emissions in para
rubber (Hevea brasiliensis Mull. Arg) plantation by DNDC model in Upland
Area Northern, Thailand
Authors: C. Podong.Computational Ecology; Software,2014,4(4):269-275
Abstract: The process-oriented model DNDC describing biogeochemical cycling of C and N and greenhouse gases (GHGs) fluxes carbon dioxide (CO2), nitrous oxide (N2O), nitric oxide (NO) in para rubber plantation was applied to simulate carbon sequestration and GHGs emissions in a para rubber plantation of small watershed in the lower part of northern Thailand. The results indicated that the simulated gross primary production (GPP) and soil organic carbon (SOC) of the para rubber plantation was strongly affected by temperature. The annual total GPP was 2,765.8 kg C /ha/yr, and net primary production (NPP) was 2,032.4. The SOC in 0-10 cm. were 4,983 kg C /ha/yr for 2011.The simulated seasonal variation in CO2 emissions generally followed the seasonal variations in temperature and precipitation. The annual total CO2 emission was 976.53 kg C /ha/yr for 2011, the simulated annual total N2O emissions from the plantation's soil was 10.51 kg N ha-1yr-1 for 2011, the annual total NO emissions were 0.87 kg N /ha/yr for 2011, and the annual Dissolved Organic Matter (DOM) leaching was 0.23 kg C /ha/yr.
- Land use change detection using remote sensing and artificial neural
network: Application to Birjand, Iran
Authors: Saeed Ahmadizadeh; Maryam Yousefi, Mehdi Saghafi.Computational Ecology Software,2014,4(4):276-288
Abstract: and is becoming a scarce natural resource due to the burgeoning population growth and urbanization. Essentially, detecting changes in land surface is significant for understanding and assessing human impacts on the environment. Nowadays, land use change detection using remote sensing data provides quantitative and timely information for management and evaluation of natural resources. This study investigates the land use changes in Birjand of Iran using Landsat TM5 images between 1986 and 2010. Artificial neural network was used for classification of Landsat images. Five land use classes were delineated include Pasture, Irrigated farming Land, Dry farming lands, Barren land and Urban. Post-classification technique applied to monitor land use change through cross-tabulation. Visual interpretation, expert knowledge of the study area and ground truth in formation accumulated with field works to assess the accuracy of the classification results. Overall accuracy of 2010 and 1986 image classification was 89.67 (Kappa coefficient: 0.8539) and 88.78 (Kappa coefficient: 0.8424) respectively. The results showed considerable land use changes for the given study area. The greatest increase was related to Barren land class almost 378 percent. The dry farming lands reduced by almost 48 percent during the study period. Urban class has increased drastically about 219 percent, 3 percent of dry farming lands, 61 percent of pastures lands, 4percent of irrigated farming land in 1986, converted to urban and industrial land in 2010 and alone 31 percent of urban land in 1986 had conformity to urban in 2010. Irrigated farming land increased about 17.16 percent predominantly due to population growth. The result of this study revealed a successful application of the ANN approach for land use change detection. Although this model demonstrated high sensitivity to training samples data, it required trial and error for attainment more accurate. But high accuracy of classification in last two years proved that ANN was highly efficient for classification of Landsat images in the study area.
- Catastrophic behavior of aphid population dynamics: An analysis of
swallowtail model
Authors: Mkdk Piyaratne; Huiyan Zhao, Zuqing Hu, Xiangshun Hu, Bailing Wang.Computational Ecology Software,2014,4(3):135-146
Abstract: Catastrophe phenomena are frequent in insect ecology, especially in aphid populations. Complexity of this phenomenon urges different modeling frameworks other than traditional methodologies to understand the trajectories of their behavior. Situations like this can be best handled using catastrophe theory. A few numbers of experiments have been conducted to develop catastrophe models in insect ecology, especially for aphids, and most of them are based on cusp catastrophe theory which is a lower dimensional model. However few attempts using higher dimensional models such as swallowtail or butterfly theory to analyze aphid population dynamics are also exist. In this paper we tried to analyze a recently developed higher dimensional catastrophe theory model (APHIDSim) in order to identify catastrophe regions, and used independent data to identify if catastrophic behavior is observed in the data and consequently to further verify the model. Here we found that identifying catastrophe regions is possible using catastrophe theory model, and it can be used to analyze catastrophes in insect ecology by graphically interpreting the simulated results. Increasing of insect population is intrinsically catastrophic and catastrophes (jumps) occur between states even if the driving variables still change smoothly. The results further verified the previously developed model, and we suggest that insect management program developers should consider this phenomenon when they design the management strategies for insect controlling.
- Covariance among independent variables determines the overfitting and
underfitting in variation partitioning methods: with a focus on the mixed
co-variation
Authors: YouHua Chen.Computational Ecology; Software,2014,4(3):147-162
Abstract: The effectiveness and validity of applying variation partitioning methods in community ecology has been questioned. Here, using mathematical deduction and numerical simulation, we made an attempt to uncover the underlying mechanisms determining the effectiveness of variation partitioning techniques. The covariance among independent variables determines the under-fitting and over-fitting problem with the variation partitioning process. Ideally, it is assumed that the covariance among independent variables will be zero (no correlation at all), however, typically there will be some colinearities. Therefore, we analyzed the role of slight covariance on influencing species variation partitioning. We concluded that when the covariance between spatial and environmental predictors is positive, all the three components-pure environmental, spatial variations and mixed covariation were over-fitted, with the sign of the true covariation being negative. In contrast, when the covariance is negative, all the three components were under-fitted with the sign of true covariation being positive. Other factors, including extra noise levels, the strengths of variable coefficients and the patterns of landscape gradients, could reduce the fitting problems caused by the covariance of variables. The conventional calculation of mixed covariation is incorrect and misleading, as the true and estimated covariations are always sign-opposite. In conclusion, I challenge the conventional three-step procedure of variation partitioning, suggesting that a full regression model with all variables together is robust enough to correctly partition variations.
- Continuous-discrete model of parasite-host system dynamics: Trigger regime
at simplest assumptions
Authors: L. V. Nedorezov; Neklyudova.Computational Ecology Software,2014,4(3):163-169
Abstract: In paper continuous-discrete model of parasite-host system dynamics is analyzed. Within the framework of model it is assumed that appearance of individuals of new generations of both populations is realized at fixed time moments tk=hk, t0=0, k=1,2,... , h=const>0; it means that several processes are compressed together: producing of eggs by hosts, attack of eggs by parasites (with respective transformation of host's eggs into parasite's eggs), staying of hosts and parasites in phase "egg", and appearance of new individuals. It is also assumed that death process of individuals has a continuous nature, but developments of both populations are realized independently between fixed time moments. Dynamic regimes of model are analyzed. In particular, it was obtained that with simplest assumptions about birth process in host population and numbers of attacked hosts regime with two non-trivial stable attractors in phase space of system can be realized.
- Towards the maturity model for feature oriented domain analysis
Authors: Muhammad Javed; Muhammad Naeem, Hafiz Abdul Wahab.Computational Ecology Software,2014,4(3):170-182
Abstract: Assessing the quality of a model has always been a challenge for researchers in academia and industry. The quality of a feature model is a prime factor because it is used in the development of products. A degraded feature model leads the development of low quality products. Few efforts have been made on improving the quality of feature models. This paper is an effort to present our ongoing work i.e. development of FODA (Feature Oriented Domain Analysis) maturity model which will help to evaluate the quality of a given feature model. In this paper, we provide the quality levels along with their descriptions. The proposed model consists of four levels starting from level 0 to level 3. Design of each level is based on the severity of errors, whereas severity of errors decreases from level 0 to level 3. We elaborate each level with the help of examples. We borrowed all examples from the material published by the research community of Software Product Lines (SPL) for the application of our framework.
- Digitizing information for wider reach through 'him-Padap-Sanklan', an
e-inventory of Himalayan flora
Authors: Amit Kumar; Sanjay Kumar Uniyal, Meenakshi, Rakesh D. Singh, Paramvir S. Ahuja.Computational Ecology Software,2014,4(3):183-192
Abstract: 'him-Padap-Sankalan' is a digital directory of floral resources of Himachal Pradesh H.P., a biologically rich state of the Himalayan Biodiversity hotspot. It provides information on nomenclature, taxonomic classification, local name(s), trade name(s) and uses of 3348 plant species along with maps showing their distribution in H.P. The information housed in 'Him-Padap-Sankalan' has been compiled from published sources, primarily the Flora of Himachal Pradesh: Analysis. The Graphic User Interface of the 'him-Padap-Sankalan' has been prepared using ASP.Net having MS-Access database in the back end. The 'scientific names', 'trade names', 'local names', 'synonyms', 'genus' and 'species' are the various search modules of 'him-Padap-Sankalan', which can be accessed using an internet browser connected through local area network. Analysis of information reveals that of the 201 families, Poaceae, Asteraceae, Papilionaceae, Scrophularariaceae, Rosaceae, Cyperaceae, Lamiaceae, Ranunculaceae, Brassicaceae and Apiaceae are the ten dominat families in the state. 24 families and 18 genera are common to all the 12 districts of H.P. The maximum number of families, genera and species are in Shimla district and the least in Bilaspur district of H.P.
- Multi Resolution Analysis (MRA) of satellite images of oil spill disasters
Authors: Rashid Hussain.Computational Ecology; Software,2014,4(3):193-204
Abstract: Oil spill disasters monitoring and mitigation requires availability of state of the art applications and tools. Conventional technology gets benefit from latest trends and research in satellite imaginary. This research highlights multi-resolution wavelet analysis of satellite images of oil spill disasters. Multi-resolution analysis is one of the powerful techniques to analyze information content of images. This analysis enables us to have a scale-invariant interpretation of the image. At each resolution level, both smooth and detailed signals carry all the necessary information to reconstruct the smooth signal at the next level. The wavelet decomposition results in detail and approximate threshold coefficients. Multi resolution wavelet decomposition is used to analyze the image in both time and frequency domain. It provides better frequency resolution and poor time resolution for lower frequency; better time resolution and poor frequency resolution for higher frequency. This condition is fortunately suited for real applications; as signals have high frequency components for very short period of the interval and low frequency components for longer durations.
- Assessment of satellite and model derived long term solar radiation for
spatial crop models: A case study using DSSAT in Andhra Pradesh
Authors: Anima Biswal; M. V. R. Sesha Sai, S. V. C. Kameswar Rao.Computational Ecology Software,2014,4(3):205-214
Abstract: Crop Simulation models are mathematical representations of the soil plant-atmosphere system that calculate crop growth and yield, as well as the soil and plant water and nutrient balances, as a function of environmental conditions and crop management practices on daily time scale. Crop simulation models require meteorological data as inputs, but data availability and quality are often problematic particularly in spatialising the model for a regional studies. Among these weather variables, daily total solar radiation and air temperature (Tmax and Tmin) have the greatest influence on crop phenology and yield potential. The scarcity of good quality solar radiation data can be a major limitation to the use of crop models. Satellite-sensed weather data have been proposed as an alternative when weather station data are not available. These satellite and modeled based products are global and, in general, contiguous in time and also been shown to be accurate enough to provide reliable solar and meteorological resource data over large regions where surface measurements are sparse or nonexistent. In the present study, an attempt was made to evaluate the satellite and model derived daily solar radiation for simulating groundnut crop growth in the rainfed distrcits of Andhra Pradesh. From our preliminary investigation, we propose that satellite derived daily solar radiation data could be used along with ground observed temperature and rainfall data for regional crop simulation studies where the information on ground observed solar radiation is missing or not available.
- Spatial risk assessment of alien plants in China using biodiversity
resistance theory
Authors: YouHua Chen.Computational Ecology; Software,2014,4(2:82-88
Abstract: In the present study, the potential occurrence risk of invasive plants across different provinces of China is studied using disease risk mapping techniques (empirical Bayesian smoothing and Poisson-Gamma model). The biodiversity resistance theory which predicts that high-biodiversity areas will have reduced risk of species invasion serves as the base for performing spatial risk assessment of plant invasion across provinces. The results show that, both risk mapping methods identified that north-eastern part of China have the highest relative risk of plant invasion. In contrast, south-western and south-eastern parts of China, which have high woody plant richness, are predicted to possess low relative risks of plant invasion. Through spatial regression analysis (simultaneous autoregression model), nine environmental variables representing energy availability, water availability, seasonality, and habitat heterogeneity are used to explain the relative risk of plant invasion across provinces of China. The fitting results suggest that, PRECrange and TEMrange are the most two important covariates correlated with the occurrence risks of alien plants at provincial level in China. As indicated by Moran's I index, spatial regression analysis can effectively eliminate the potential biases caused by spatial autocorrelation.
- Stability analysis of a discrete ecological model
Authors: Q. Din; E. M. Elsayed.Computational Ecology Software,2014,4(2:89-103
Abstract: In this paper, we study the qualitative behavior of following discrete-time population model: x(n+1)=a+bx(n)+rx(n-1)exp(-y(n)),y(n-1)=g+ey(n)+hy(n-1)exp(-x(n)), where parameters a, b, r, g, e, h and initial conditions x(0), x(-1), y(0), y(-1) are positive real numbers. More precisely, we investigate the existence and uniqueness of positive equilibrium point,boundedness character, persistence, local asymptotic stability, global behavior and rate of convergence of unique positive equilibrium point of this model. Some numerical examples are given to verify our theoretical results.
- Qualitative behavior of an anti-competitive system of third-order rational
difference equations
Authors: Q. Din; M. N. Qureshi, A. Q. Khan.Computational Ecology Software,2014,4(2:104-115
Abstract: In this paper, our aim is to study the equilibrium points, local asymptotic stability, global behavior of an equilibrium points and rate of convergence of an anti-competitive system of third-order rational difference equations of the form: x(n+1)=ay(n-2)/[b+rx(n)x(n-1)x(n-2)], y(n+1)=cx(n-2)/[d+hy(n)y(n-1)y(n-2)], n=0,1,2,..., where the parameters a, b, c, d, r, h and initial conditions x(0), x(-1), x(-2), y(0), y(-1), y(-2) are positive real numbers. Some numerical examples are given to verify our theoretical results.
- Complex dynamics of a stochastic discrete modified Leslie-Gower
predator-prey model with Michaelis-Menten type prey harvesting
Authors: A. Elhassanein.Computational Ecology; Software,2014,4(2:116-128
Abstract: This paper introduced a stochastic discretized version of the modified Leslie-Gower predator-prey model with Michaelis-Menten type prey harvesting. The dynamical behavior of the proposed model was investigated. The existence and stability of the equilibria of the skeleton were studied. Numerical simulations were employed to show the model's complex dynamics by means of the largest Lyapunov exponents, bifurcations, time series diagrams and phase portraits. The effects of noise intensity on its dynamics and the intermittency phenomenon were also discussed via simulation.
- Synthetic Aperture Radar (SAR) image segmentation by fuzzy c-means
clustering technique with thresholding for iceberg images
Authors: Usman Seljuq; Rashid Hussain.Computational Ecology Software,2014,4(2:129-134
Abstract: Fuzzy c-means (FCM) clustering algorithm is widely used for image segmentation. The purpose of clustering is to identify natural groupings of data from a large data set, which results in concise representation of system's behavior. It can be used to detect icebergs regardless of ambient conditions like rain, darkness and fog. As a result SAR images can be used for iceberg surveillance. In this paper we have investigate FCM with thresholding for iceberg image segmentation for Synthetic Aperture Radar (SAR) images. The results showed that the assessment parameters; mean and entropy have lower values for efficient segmentation.
- About a non-parametric model of hermaphrodite population dynamics
Authors: L.V. Nedorezov.Computational Ecology; Software,2014,4(1):1-11
Abstract: In current publication non-parametric model (model of Kolmogorov's type) of hermaphrodite population dynamics is analyzed. It is assumed that there are four basic variables: number of individuals, number of pairs, and number of pregnant individuals. It is also assumed that number of pairs is fast variable: it allows decreasing of number of differential equations. For conditions of pure qualitative type for birth and death rates of individuals in population possible dynamic regimes are determined.
- Temporal mortality-colonization dynamic can influence the coexistence and
persistence patterns of cooperators and defectors in an evolutionary game
model
Authors: YouHua Chen; XueKe Lu, YouFang Chen.Computational Ecology Software,2014,4(1):12-21
Abstract: In the present report, the coexistence and persistence time patterns of Prisoners' Dilemma game players were explored in 2D spatial grid systems by considering the impacts of the mortality-colonization temporal dynamic specifically. Our results showed that the waiting time for triggering a colonization event could remarkably influence and change the extinction patterns of both cooperators and defectors. Interestingly, a relatively high frequency of stochastic colonization events could promote the persistence of defectors but not cooperators. In contrast, a low frequency of stochastic- or constant-time colonization events could facilitate the persistence of cooperators but not defectors. However, a long waiting time would be detrimental to the survival of both game players and drives them to go extinction in faster rates. At last, it was found that colonization strength played a relatively weak role on influencing the coexistence scenarios of both game players, but should be kept small if the coexistence of game players is needed to maintain. In conclusion, our study provides evidence showing that the temporal trade-off of mortality and colonization activities would influence the evolution of PD game and the persistence of cooperators and defectors.
- An online calculator for spatial data and its applications
Authors: Kalle Remm; Tiiu Kelviste.Computational Ecology Software,2014,4(1):22-34
Abstract: An online calculator (http://digiarhiiv.ut.ee/kalkulaator/) for statistical analysis of spatial data is introduced. The calculator is applicable in a wide range of spatial research and for courses involving spatial data analysis. The present version of the calculator contains 35 web pages for statistical functions with several options and settings. The input data for most functions are pure Cartesian coordinates and variable values, which should becopied to the input cell on the page of a particular spatial operation. The source code for the computational part of all functions is freely available in C# programming language. Examples are given for thinning spatially dense observation points to a predefined minimum distance, for calculating spatial autocorrelations, for creating habitat suitability maps and for generalising movement data into spatio-temporal clusters.
- Global behavior of an anti-competitive system of fourth-order rational
difference equations
Authors: A. Q. Khan; Q. Din, M. N. Qureshi, T. F. Ibrahim.Computational Ecology Software,2014,4(1):35-46
Abstract: In the present work, we study the qualitative behavior of an anti-competitive system of fourth-order rational difference equations. More precisely, we study the local asymptotic stability, global character of the unique equilibrium point, and the rate of convergence of the positive solutions of the given system. Some numerical examples are given to verify our theoretical results.
- Effect of land uses of Huai Lam Kradon Sub-watershed on quantifying soil
carbon potential with process base model
Authors: Chattanong Podong; Roongreang Poolsiri.Computational Ecology Software,2014,4(1):47-62
Abstract: The study the effect of land use on soil carbon is importantly for the future management of greenhouse gases and climate change, and soil carbon budget is one activity mention of the United Nations Framework Convention on Climate Change (UNFCCC) for decreasing effect from climate change. Previous studies based on field observations have provided direct information about soil carbon storage and fluxes at specific sites, but soil carbon is highly dynamic in space and time and that is driven by complex combinations of hydrology, soil vegetation and management condition. The observation results was soil carbon higher in mixed deciduous forest 17,472.30 Kg C/ha than para rubber plantation 8,304.52 Kg C /ha at depth 0-5 cm and at depth 5-20 cm 8,304.52 Kg C /ha and 6,776.65, respectively. The DNDC model has shown that it can perform well in its representation of the effects of both land uses change in this study area. Simulation results showed significant loss of soil carbon from system under both land use types and eight scenarios of land use change from mixed deciduous forest to para rubber plantation and para rubber tree change to mixed deciduous forest. The annual 50 year soil carbon was 17,960 and 8,300 C /ha/yr for mixed deciduous forest and para rubber plantation, respectively. The simulated soil carbon under land uses change scenarios. The result for soil carbon content in three scenarios for mixed deciduous forest change to para rubber plantation scenarios. The soil carbon decrease in all scenarios and the mean decrease highest of litter carbon in MDF 10 Year to Para rubber 40 Year scenario was 8,770.42 C /ha/yr or 49.79% and mean lowest of soil carbon MDF 40 Year to Para rubber 10 Year scenario was 4,700.47 /ha/yr or 26.68 %. The result for soil carbon content in three scenarios for mixed deciduous forest change to para rubber plantation scenarios. The mean soil carbon and decrease highest of litter carbon in para rubber plantation 10 year change to mixed deciduous forest 40 year was 6931.22 C /ha/yr or 45.57% and mean lowest of soil carbon para rubber plantation 40 year change to mixed deciduous forest 10 year was 3452.57 C /ha/yr or 22.70%.
- Analytical treatment of system of KdV equations by Homotopy Perturbation
Method (HPM) and Homotopy Analysis Method (HAM)
Authors: Hafiz Abdul Wahab; Tahir Khan, Muhammad Shakil, Saira Bhatti, Muhammad Naeem.Computational Ecology Software,2014,4(1):63-81
Abstract: In this article the Homotopy Perturbation Method (HPM) and Homotopy Analysis Method (HAM) are applied to obtain analytic approximate solution to three system of nonlinear wave equations, namely two component evolutionary system of a homogeneous KdV Equations of order three (system-I) as well as (system-II) and the generalized coupled Hirota Satsuma KdV (System-III).
