Computational Ecology and Software (ISSN 2220-721X)
http://www.iaees.org/publications/journals/ces/ces.asp
International Academy of Ecology and Environmental SciencesComputational Ecology and Software (ISSN 2220-721X); Publisher: International Academy of Ecology and Environmental Sciences; Address: Unit 3, 6/F., Kam Hon Industrial Building, 8 Wang Kwun Road, Kowloon Bay, Hong Kong; Tel: 00852-2138 6086; Fax: 00852-3069 1955; E-mail: office@iaees.orgWhat is RSS
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Computational Ecology and Software
http://www.iaees.org/publications/journals/ces/online-version.asp
International Academy of Ecology and Environmental Sciences
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(1)/Using-data-clustering-as-a-method-of-estimating-the-risk.pdf
Watts MJ. Computational Ecology and Software,2011,1(1):1-13
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(1)/Are-individual-based-models-a-suitable-approach.pdf
Griebeler EM. Computational Ecology and Software,2011,1(1):14-24
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(1)/Analysis-of-some-experimental-time-series-by-Gause.pdf
Nedorezov LV. Computational Ecology and Software,2011,1(1):25-36
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(1)/Simulation-of-arthropod-abundance-from-plant-composition.pdf
Zhang WJ. Computational Ecology and Software,2011,1(1):37-48
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(1)/Evaluating-a-Bayesian-approach-to-improve-accuracy.pdf
Stafford R, Lloyd JR. Computational Ecology and Software,2011,1(1):49-54
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(1)/Fuzzy-cognitive-maps-outmatch-loop-analysis.pdf
Ferrarini A. Computational Ecology and Software,2011,1(1):55-59
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(1)/Quantitative-risk-analysis-and-prediction-of-potential-distribution-areas.pdf
Lui XR. Computational Ecology and Software,2011,1(1):60-65
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(1)/An-emerging-ecological-science.pdf
Zhang WJ. Computational Ecology and Software,2011,1(1):66-67
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(1)/Computational-Ecology-ANNs.pdf
Zheng H. Computational Ecology and Software,2011,1(1):68
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(2)/Combined-use-of-weather-forecasting-and-satellite.pdf
Wolfgang Knorr, Ioannis Pytharoulis, George P. Petropoulos, Nadine Gobron. Computational Ecology and Software,2011,1(2):112-120
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(2)/Detecting-ecological-breakpoints.pdf
Alessandro Ferrarini. Computational Ecology and Software,2011,1(2):121-124
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(2)/Wavelet-analysis-to-detect-regime-shifts.pdf
C. Gaucherel. Computational Ecology and Software,2011,1(2):69-85
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(2)/About-a-modification-of-Beddington-Free-Lawton-model.pdf
P.V. Ivanchikov, L.V. Nedorezov. Computational Ecology and Software,2011,1(2):86-94
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(2)/Use-of-geospatial-technology-in-evaluating-landscape.pdf
Ekwal Imam. Computational Ecology and Software,2011,1(2):95-111
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(3)/Measuring-competition-in-plant-communities.pdf
Christian Damgaard. Computational Ecology and Software,2011,1(3):125-137
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(3)/Improving-cluster-based-methods.pdf
Michael J. Watts, Susan P. Worner. Computational Ecology and Software,2011,1(3):138-145
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 by
their 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
http://www.iaees.org/publications/journals/ces/articles/2011-1(3)/Complexity-analysis-in-particulate-matter-measurements.pdf
Luciano Telesca, Michele Lovallo. Computational Ecology and Software,2011,1(3):146-152
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(3)/Some-aspects-of-animal-behavior-and-community-dynamics.pdf.pdf
Vikas Rai, R. K. Upadhyay, S. N. Raw, Nitu Kumari. Computational Ecology and Software,2011,1(3): 153-182
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(3)/Java-program-non-parametric-statistic-comparison-community-structure.pdf
WenJun Zhang. Computational Ecology and Software,2011,1(3): 183-185
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(3)/A-new-fuzzy-algorithm-for-ecological-ranking.pdf
Alessandro Ferrarini. Computational Ecology and Software,2011,1(3): 186-188
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(4)/estimating-critical-abundance-thresholds.pdf
Rishi Sharma, Scott W. Raborn. Computational Ecology and Software, 2011, 1(4):189-207
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(4)/about-a-dynamic-model-of-interaction-of-insect-population.pdf
L.V. Nedorezov. Computational Ecology and Software, 2011, 1(4):208-217
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(4)/estimating-survival-rates-in-ecological-studies.pdf
Christian Damgaard, Adeline Fayolle. Computational Ecology and Software, 2011, 1(4):218-223
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(4)/comparison-of-numerical-simulations-of-reactive-transport.pdf
I. Haidar, F. Gerard, A. Rapaport. Computational Ecology and Software, 2011, 1(4):224-239
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(4)/a-fitter-use-of-Monte-Carlo-simulations.pdf
Alessandro Ferrarini. Computational Ecology and Software, 2011, 1(4):240-243
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
http://www.iaees.org/publications/journals/ces/articles/2011-1(4)/computer-generation-of-initial-spatial-distribution.pdf
GuangHua Liu, WenJun Zhang. Computational Ecology and Software, 2011, 1(4):244-248
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
http://www.iaees.org/publications/journals/ces/articles/2012-2(1)/spatiotemporal-pattern-induced-by-self-and-cross-diffusion.pdf
Ranjit Kumar Upadhyay, N. K. Thakur.Computational Ecology and Software,2012,2(1):1-25
In this paper, we have made an attempt to provide a unified framework to understand the complex
spatiotemporal patterns induced by self and cross diffusion in a spatial Holling-Tanner model for
phytoplankton-zooplankton-fish interaction. The effect of critical wave length which can drive the system to
instability 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 conditions
and 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 mixture
patterns prevail over the whole domain on increasing the values of self- diffusion coefficients of phytoplankton
and zooplankton and the dynamics of the system do not undergo any further changes.
System dynamic approach for management of urban parks: a case study
http://www.iaees.org/publications/journals/ces/articles/2012-2(1)/system-dynamic-approach-for-management-of-urban-parks.pdf
Lucia Tamburino, Valentina La Morgia, Ezio Venturino.Computational Ecology and Software,2012,2(1):26-41
Public agencies tackling the issues of natural resource management need objective analysis to anticipate the
ecosystem consequences of their actions. Mathematical models can be regarded as an effective tool to support
decision makers in this context because of their predictive capacity and of their ability to describe complex
natural systems. In particular, the aim of this paper is to show how mathematical modelling and simulation can
be applied in the field of urban park management. As an example, we consider a case study where a domestic
herbivore, the sheep, was introduced as a natural regulator of grass growth. The results show that the
introduction of sheep is not currently sustainable and that it should be complemented by other measures in
order 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
http://www.iaees.org/publications/journals/ces/articles/2012-2(1)/modification-May-model-of-parasite-host-system.pdf
P.V. Ivanchikov, L.V. Nedorezov.Computational Ecology and Software,2012,2(1):42-52
Current publication is devoted to the construction of modification of well-known May 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
binomial 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.
Assessing ballast treatment standards for effect on rate of establishment using a stochastic model of the green crab
http://www.iaees.org/publications/journals/ces/articles/2012-2(1)/assessing-ballast-treatment-standards-for-effect.pdf
Cynthia Cooper, Carlton D. Hunt, Cheryl Dingus, P. Scott Libby, Greg Kirkbride.Computational Ecology and Software,2012,2(1):53-69
This paper describes a stochastic model used to characterize the probability/risk of NIS establishment from
ships' ballast water discharges. Establishment is defined as the existence of a sufficient number of individuals
of a species to provide for a sustained population of the organism. The inherent variability in population
dynamics of organisms in their native or established environments is generally difficult to quantify. Much
qualitative information is known about organism life cycles and biotic and abiotic environmental pressures on
the population, but generally little quantitative data exist to develop a mechanistic model of populations in
such complex environments. Moreover, there is little quantitative data to characterize the stochastic
fluctuations of population size over time even without accounting for systematic responses to biotic and abiotic
pressures. This research applies an approach using life-stage density and fecundity measures reported in
research to determine a stochastic model of an organism's population dynamics. The model is illustrated with
data from research studies on the green crab that span a range of habitats of the established organism and were
collected over some years to represent a range of time-varying biotic and abiotic conditions that are expected
to exist in many receiving environments. This model is applied to introductions of NIS at the IMO D-2 and the
U.S. ballast water discharge standard levels designated as Phase Two in the United States Coast Guard's
Notice of Proposed Rulemaking. Under a representative range of ballast volumes discharged at U.S. ports, the
average 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 water
discharge. The longevity of populations from the untreated ballast water discharges is expected to be reduced
by 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
http://www.iaees.org/publications/journals/ces/articles/2012-2(1)/using-artificial-neural-networks-to-predict-the-distribution.pdf
Michael J. Watts, Susan P. Worner.Computational Ecology and Software,2012,2(1):70-79
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
http://www.iaees.org/publications/journals/ces/articles/2012-2(1)/program-for-statistic-test-of-community-evenness.pdf
WenJun Zhang, Hao Zheng.Computational Ecology and Software,2012,2(1):80-82
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
http://www.iaees.org/publications/journals/ces/articles/2012-2(2)/modeling-and-analysis-of-some-methods.pdf
L.V. Nedorezov.Computational Ecology and Software,2012,2(2):83-95
In current publication the stochastic model of individual migrations within the limits of closed domain and
processes of data collections using in entomology are considered. The behavior of data variation with respect
to changing of population size is analyzed. In particular, it was shown that dependence of standard deviations
has a non-linear character under the population density increasing. It was also shown that confidence level to
datasets of population density which were obtained with traditional methods and under the low value of
population density must be extremely low.
Improving Eastern Bluebird nest box performance using computer analysis of
satellite images
http://www.iaees.org/publications/journals/ces/articles/2012-2(2)/improving-eastern-bluebird-nest-box-performance.pdf
Sarah Svatora, Lior Shamir.Computational Ecology and Software,2012,2(2):96-102
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 by
Eastern Bluebirds (Sialia sialis) in Michigan can be improved by about 48%. The analysis is based on a strong
correlation 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 taken
from Google Earth, and can be used by conservationists to select a box placement strategy that will optimize
the efficacy of the boxes deployed in a given area.
Permutation tests to estimate significances on Principal Components Analysis
http://www.iaees.org/publications/journals/ces/articles/2012-2(2)/permutation-tests-to-estimate-significances.pdf
Vasco M. N. C. S. Vieira.Computational Ecology and Software,2012,2(2):103-123
Principal Component Analysis is the most widely used multivariate technique to summarize information in a
data collection with many variables. However, for it to be valid and useful the meaningful information must be
retained and the noisy information must be sorted out. To achieve it an index from the original data set is
estimated, after which three classes of methodologies may be used: (i) the analytical solution to the distribution
of the index under the assumption the data has a multivariate normal distribution, (ii) the numerical solution to
the distribution of the index by means of permutation tests without any assumption about the data distribution
and (iii) the bootstrap numerical solution to the percentiles of the index and the comparison to its assumed
value for the null hypothesis without any assumption about the data distribution. New indices are proposed to
be used with permutation tests and compared with previous ones from application to several data sets. Their
advantages and draw-backs are discussed together with the adequacy of permutation tests and inadequacy of
both bootstrap techniques and methods that rely on the assumption of multivariate normal distributions.
Dynamical complexities in a discrete-time food chain
http://www.iaees.org/publications/journals/ces/articles/2012-2(2)/dynamical-complexities-in-a-discrete-time-food-chain.pdf
Abd-Elalim A. Elsadany.Computational Ecology and Software,2012,2(2):124-139
In this paper, a discrete-time food chain characterized by three species is modeled by a system of three
nonlinear difference equations. The existence and local stability of the equilibrium points of the discrete
dynamical system are analyzed. It is shown that for some parameter values the interior equilibrium point loses
its stability through a discrete Hopf bifurcation. Basic properties of the discrete system are analyzed by means
of phase portraits, bifurcation diagrams and Lyapunov exponents. We have varied the result through numerical
calculation.
A novel approach for modeling malaria incidence using complex categorical
household data: The minimum message length (MML) method applied to
Indonesian data
http://www.iaees.org/publications/journals/ces/articles/2012-2(3)/a-novel-approach-for-modeling-malaria-incidence.pdf
Gerhard Visser, Pat Dale, David Dowe, Ermi Ndoen, Mike Dale, Neil Sipe.Computational Ecology and Software,2012,2(3):140-159
We investigated the application of a Minimum Message Length (MML) modeling approach to identify the
simplest model that would explain two target malaria incidence variables: incidence in the short term and on
the average longer term, in two areas in Indonesia, based on a range of ecological variables including
environmental and socio-economic ones. The approach is suitable for dealing with a variety of problems such
as complexity and where there are missing values in the data. It can detect weak relations, is resistant to overfitting
and can show the way in which many variables, working together, contribute to explaining malaria
incidence. This last point is a major strength of the method as it allows many variables to be analysed. Data
were obtained at household level by questionnaire for villages in West Timor and Central Java. Data were
collected 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, household
characteristics, socio-economic status and perception of malaria cause. Several models were used and the
simplest (best) model, that is the one with the minimum message length was selected for each area. The results
showed that consistent predictors of malaria included combinations of ecology (coastal), preventative (clean
backyard) and environment (mosquito breeding place, garden and rice cultivation). The models also showed
that most of the other variables were not good predictors and this is discussed in the paper. We conclude that
the method has potential for identifying simple predictors of malaria and that it could be used to focus malaria
management on combinations of variables rather than relying on single ones that may not be consistently
reliable.
A fuzzy mathematics approach in measuring air pollution from motor
vehicles
http://www.iaees.org/publications/journals/ces/articles/2012-2(3)/a-fuzzy-mathematics-approach-in-measuring-air-pollution.pdf
Soumak Biswas, Sripati Jha, Ramayan Singh.Computational Ecology and Software,2012,2(3):160-168
Air pollution from motor vehicle in cities specially in developing countries has been a major source of urban
air pollution and hence a cause of concern for the administrators of the cities as well as for researchers in the
field of ecology and mathematics. In the present work, the fuzzy membership functions for some of the
attributes regarding air pollution from motor vehicle are proposed. To study the index of air pollution in
different area of a city, the air pollution index is proposed, which takes into account the membership function
for 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 of
the city under certain assumptions. The effectiveness and suitability of the method is established by taking an
example.
Chaos and bifurcation of a nonlinear discrete prey-predator system
http://www.iaees.org/publications/journals/ces/articles/2012-2(3)/chaos-and-bifurcation-of-a-nonlinear-discrete-prey-predator-system.pdf
Abd-Elalim A. Elsadany, H. A. EL-Metwally, E. M. Elabbasy, H. N. Agiza.Computational Ecology and Software,2012,2(3):169-180
The discrete-time Prey-predator system obtained by two dimensional map was studied in present study. The
fixed points and their stability were analyzed. Bifurcation diagram has been obtained for selected range of
different parameters. As some parameters varied, the model exhibited chaos as a long time behavior. Lyapunov
exponents and fractal dimension of the chaotic attractor of our map were also calculated. Complex dynamics
such as cycles and chaos were observed.
Bayesian parameter estimation in dynamic population model via particle
Markov chain Monte Carlo
http://www.iaees.org/publications/journals/ces/articles/2012-2(4)/bayesian-parameter-estimation-in-dynamic-population-model.pdf
Meng Gao, XingHua Chang, XinXiu Wang.Computational Ecology and Software,2012,2(4):181-197
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
http://www.iaees.org/publications/journals/ces/articles/2012-2(4)/fluctuations-of-population-dynamics-model-parameters.pdf
L. V. Nedorezov.Computational Ecology and Software,2012,2(4):198-212
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
http://www.iaees.org/publications/journals/ces/articles/2012-2(4)/a-new-model-for-ecological-ranking-and-evaluation.pdf
Alessandro Ferrarini.Computational Ecology and Software,2012,2(4):213-219
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 evaluation
of 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
http://www.iaees.org/publications/journals/ces/articles/2012-2(4)/synthetic-aperture-radar-images-features-clustering.pdf
Rashid Hussain.Computational Ecology and Software,2012,2(4):220-225
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 in
remote sensing images for ecological monitoring.
The role of aerosols to increase rainfall in the regions with less intensity rain:
A modeling study
http://www.iaees.org/publications/journals/ces/articles/2013-3(1)/the-role-of-aerosols-to-increase-rainfall.pdf
Shyam Sundar, Rajan K. Sharma.Computational Ecology and Software,2013,3(1):1-8
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 to
support analytical results.
Evaluation of land use/land cover changes in Mekelle City, Ethiopia using
Remote Sensing and GIS
http://www.iaees.org/publications/journals/ces/articles/2013-3(1)/evaluation-of-land-use-land-cover-changes.pdf
Mary Tahir, Ekwal Imam, Tahir Hussain.Computational Ecology and Software,2013,3(1):9-16
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(2)/Landscape-Builder-software-for-creation-of-initial-landscapes.pdf
William Dijak.Computational Ecology and Software,2013,3(2):17-25
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(2)/MBI-an-R-package-for-calculating-beta-diversity-indices.pdf
YouHua Chen.Computational Ecology and Software,2013,3(2):26-32
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(2)/an-nonlinear-model-for-removal-of-carbon-dioxide.pdf
Shyam Sundar.Computational Ecology and Software,2013,3(2):33-43
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(3)/estimating-significances-of-differences-between-slopes.pdf
Vasco M. N. C. S. Vieira, Joel Creed.Computational Ecology and Software,2013,3(3):44-52
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(3)/fractal-basins-in-an-ecological-model.pdf
I. Djellit, S. Chouit.Computational Ecology and Software,2013,3(3):53-60
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(3)/machine-learning-algorithms-for-predicting-roadside-particulate-matter.pdf
Yin Zhao, Yahya Abu Hasan.Computational Ecology and Software,2013,3(3):61-73
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(3)/computing-the-uncertainty-associated-with-biosystems-control.pdf
Alessandro Ferrarini.Computational Ecology and Software,2013,3(3):74-80
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(4)/dynamics-of-pinehawkmoth-stationary-dynamical-regime.pdf
L.V. Nedorezov.Computational Ecology and Software,2013,3(4):81-90
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(4)/bootstrap-estimation-of-resource-selection-probability-functions.pdf
Sandra V. Cardozo, Bryan F. J. Manly, Raydonal Ospina, Carlos T. S. Dias.Computational Ecology and Software,2013,3(4):91-101
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(4)/significances-of-differences-between-slopes-replicated-time-series-upgrade.pdf
Vasco M. N. C. S. Vieira, Joel Creed.Computational Ecology and Software,2013,3(4):102-109
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(4)/study-on-Lotka-Voltera-type-of-PDEs-through-perturbation-methods.pdf
H. A. Wahab, M. Shakil, T. Khan, S. Bhatti, M. Naeem.Computational Ecology and Software,2013,3(4):110-125
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
http://www.iaees.org/publications/journals/ces/articles/2013-3(4)/ecological-significance-of-core-buffer-and-transition-boundaries.pdf
Anima Biswal, A Jeyaram, Sumit Mukherjee, Umesh Kumar.Computational Ecology and Software,2013,3(4):126-137
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.
About a non-parametric model of hermaphrodite population dynamics
http://www.iaees.org/publications/journals/ces/articles/2014-4(1)/non-parametric-model-of-hermaphrodite-population-dynamics.pdf
L.V. Nedorezov.Computational Ecology and Software,2014,4(1):1-11
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(1)/coexistence-and-persistence-patterns-in-evolutionary-game-model.pdf
YouHua Chen, XueKe Lu, YouFang Chen.Computational Ecology and Software,2014,4(1):12-21
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(1)/an-online-calculator-for-spatial-data.pdf
Kalle Remm, Tiiu Kelviste.Computational Ecology and Software,2014,4(1):22-34
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 be
copied 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
http://www.iaees.org/publications/journals/ces/articles/2014-4(1)/global-behavior-of-an-anti-competitive-system.pdf
A. Q. Khan, Q. Din, M. N. Qureshi, T. F. Ibrahim.Computational Ecology and Software,2014,4(1):35-46
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(1)/effect-of-land-uses-on-soil-carbon-potential-with-process-base-model.pdf
Chattanong Podong, Roongreang Poolsiri.Computational Ecology and Software,2014,4(1):47-62
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)
http://www.iaees.org/publications/journals/ces/articles/2014-4(1)/KdV-equations-by-Homotopy-Perturbation-Method.pdf
Hafiz Abdul Wahab, Tahir Khan, Muhammad Shakil, Saira Bhatti, Muhammad Naeem.Computational Ecology and Software,2014,4(1):63-81
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).
Spatial risk assessment of alien plants in China using biodiversity
resistance theory
http://www.iaees.org/publications/journals/ces/articles/2014-4(2)/spatial-risk-assessment-of-alien-plants.pdf
YouHua Chen.Computational Ecology and Software,2014,4(2):82-88
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(2)/stability-analysis-of-a-discrete-ecological-model.pdf
Q. Din, E. M. Elsayed.Computational Ecology and Software,2014,4(2):89-103
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(2)/qualitative-behavior-of-an-anti-competitive-system-of-difference-equations.pdf
Q. Din, M. N. Qureshi, A. Q. Khan.Computational Ecology and Software,2014,4(2):104-115
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(2)/dynamics-of-a-stochastic-discrete-modified-Leslie-Gower-model.pdf
A. Elhassanein.Computational Ecology and Software,2014,4(2):116-128
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(2)/SAR-image-segmentation-by-fuzzy-c-means-clustering.pdf
Usman Seljuq, Rashid Hussain.Computational Ecology and Software,2014,4(2):129-134
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.
Catastrophic behavior of aphid population dynamics: An analysis of
swallowtail model
http://www.iaees.org/publications/journals/ces/articles/2014-4(3)/catastrophic-behavior-of-aphid-population-dynamics.pdf
Mkdk Piyaratne, Huiyan Zhao, Zuqing Hu,Xiangshun Hu, Bailing Wang.Computational Ecology and Software,2014,4(3):135-146
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(3)/covariance-among-independent-variables-determines-the-overfitting.pdf
YouHua Chen.Computational Ecology and Software,2014,4(3):147-162
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(3)/continuous-discrete-model-of-parasite-host-system-dynamics.pdf
L. V. Nedorezov, Neklyudova.Computational Ecology and Software,2014,4(3):163-169
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(3)/maturity-model-for-feature-oriented-domain-analysis.pdf
Muhammad Javed, Muhammad Naeem, Hafiz Abdul Wahab.Computational Ecology and Software,2014,4(3):170-182
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(3)/digitizing-information-for-wider-reach.pdf
Amit Kumar, Sanjay Kumar Uniyal, Meenakshi, Rakesh D. Singh, Paramvir S. Ahuja.Computational Ecology and Software,2014,4(3):183-192
'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
http://www.iaees.org/publications/journals/ces/articles/2014-4(3)/resolution-analysis-satellite-images-of-oil-spill-disasters.pdf
Rashid Hussain.Computational Ecology and Software,2014,4(3):193-204
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(3)/satellite-and-model-derived-long-term-solar-radiation.pdf
Anima Biswal, M. V. R. Sesha Sai, S. V. C. Kameswar Rao.Computational Ecology and Software,2014,4(3):205-214
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.
Siplab, a spatial individual-based plant modelling system
http://www.iaees.org/publications/journals/ces/articles/2014-4(4)/Siplab-spatial-individual-based-plant-modelling-system.pdf
Oscar Garcia.Computational Ecology and Software,2014,4(4):215-222
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(4)/ecological-connectivity.pdf
Alessandro Ferrarini.Computational Ecology and Software,2014,4(4):223-233
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?
http://www.iaees.org/publications/journals/ces/articles/2014-4(4)/a-model-of-biological-population-data-collection.pdf
L. V. Nedorezov.Computational Ecology and Software,2014,4(4):234-247
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(4)/modeling-dynamics-of-carbon-dioxide-removal.pdf
Shyam Sundar, Ram Naresh, Ashish Kumar Mishra, Agraj Tripathi.Computational Ecology and Software,2014,4(4):248-268
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(4)/estimate-of-soil-organic-carbon-and-greenhouse-gas-emissions.pdf
C. Podong.Computational Ecology and Software,2014,4(4):269-275
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
http://www.iaees.org/publications/journals/ces/articles/2014-4(4)/land-use-detection-using-remote-sensing-and-ANN.pdf
Saeed Ahmadizadeh, Maryam Yousefi, Mehdi Saghafi.Computational Ecology and Software,2014,4(4):276-288
Land 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.
Generating and prioritizing optimal paths using ant colony
optimization
http://www.iaees.org/publications/journals/ces/articles/2015-5(1)/optimal-paths-using-ant-colony-optimization.pdf
Mukesh Mann, Om Prakash Sangwan.Computational Ecology and Software,2015,5(1):1-15
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(1)/turing-Non-Turing-patterns-in-diffusive-plankton-model.pdf
N. K. Thakur, R. Gupta, R. K. Upadhyay.Computational Ecology and Software,2015,5(1):16-27
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 spatially
distributed 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
http://www.iaees.org/publications/journals/ces/articles/2015-5(1)/chaotic-dynamics-in-discrete-time-predator-prey-food-chain.pdf
S. M. Sohel Rana.Computational Ecology and Software,2015,5(1):28-47
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(1)/local-stability-of-an-open-access-anchovy-fishery-model.pdf
M. N. Qureshi, A. Q. Khan.Computational Ecology and Software,2015,5(1):48-62
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(1)/incorporating-climatic-change-into-ecological-connectivity.pdf
Alessandro Ferrarini.Computational Ecology and Software,2015,5(1):63-68
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(1)/cardinality-based-service-feature-diagrams.pdf
Ghulam Mustafa Assad, Muhammad Naeem, Hafiz Abdul Wahab.Computational Ecology and Software,2015,5(1):69-76
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(1)/maturity-model-for-feature-oriented-domain-analysis.pdf
M. Javed, M. Naeem, H. A. Wahab.Computational Ecology and Software,2015,5(1):77-112
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(1)/Open-Source-software-on-the-environmental-protection.pdf
D. Viduka, A. Basic.Computational Ecology and Software,2015,5(1):113-118
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.
Fluctuating asymmetry and developmental instability in Protoreaster
nodosus (Chocolate Chip Sea Star) as a biomarker for environmental
stress
http://www.iaees.org/publications/journals/ces/articles/2015-5(2)/fluctuating-asymmetry-and-developmental-instability-in-Protoreaster-nodosus.pdf
D.J. V. Trono, R. Dacar, L. Quinones, S. R. M. Tabugo.Computational Ecology and Software,2015,5(2):119-129
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(2)/distinguishing-niche-and-neutral-processes.pdf
Youhua Chen.Computational Ecology and Software,2015,5(2):130-138
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(2)/homotopy-perturbation-method-to-Navier-Stokes-equations.pdf
H. A. Wahab, Anwar Jamal, Saira Bhatti, Muhammad Naeem, Muhammad Shahzad, Sajjad
Hussain.Computational Ecology and Software,2015,5(2):139-151
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(2)/modeling-the-effect-of-pollution-on-biological-species.pdf
B. Dubey, J. Hussain, S. N. Raw, Ranjit Kumar Upadhyay.Computational Ecology and Software,2015,5(2):152-174
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(2)/Hopf-bifurcation-and-stability-analysis-for-delayed-logistic-equation.pdf
E.M. Elabbasy, Waleed A.I. Elmorsi.Computational Ecology and Software,2015,5(2):175-186
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(2)/bifurcation-of-a-discrete-time-predator-prey-system.pdf
S. M. Sohel Rana.Computational Ecology and Software,2015,5(2):187-200
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(2)/modeling-survival-of-a-biological-species.pdf
Shyam Sundar, Ram Naresh.Computational Ecology and Software,2015,5(2):201-221
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.
Bifurcation and complex dynamics of a discrete-time predator-prey
system involving group defense
http://www.iaees.org/publications/journals/ces/articles/2015-5(3)/bifurcation-and-complex-dynamics-of-a-predator-prey-system.pdf
S. M. Sohel Rana.Computational Ecology and Software,2015,5(3):222-238
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(3)/impact-of-environmental-factors-on-maintaining-water-quality.pdf
Moitreyee Banerjee, Joyita Mukherjee, Arnab Banerjee, Madhumita Roy, Goutam Bandyopdhyay,
Santanu Ray.Computational Ecology and Software,2015,5(3):239-253
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(3)/measuring-the-complex-behavior-of-SO2-oxidation-reaction.pdf
Muhammad Shahzad, Sumaira Rehman, Rabia Bibi, Hafiz Abdul Wahab, Saleem Abdullah, Sarfraz
Ahmed.Computational Ecology and Software,2015,5(3):254-270
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.
Pattern recognition and simulation in ecology
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/pattern-recognition-and-simulation-in-ecology.pdf
Xiaozhuo Han, Meng Gao, Cang Hui.Computational Ecology and Software,2015,5(4):271-275
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/particle-swarm-optimization-algorithm-for-parameter-estimation.pdf
Feixia Lu, Dingyuan Mo, Meng Gao.Computational Ecology and Software,2015,5(4):276-285
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/spatial-distributions-of-niche-constructing-populations.pdf
Xiaozhuo Han, Yaling Huang, Cang Hui.Computational Ecology and Software,2015,5(4):286-298
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/effect-of-spatial-structure-on-evolution-of-cooperation.pdf
Hui Zhang, Meng Gao.Computational Ecology and Software,2015,5(4):299-316
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/architecture-of-antagonistic-networks.pdf
Savannah Nuwagaba, Cang Hui.Computational Ecology and Software,2015,5(4):317-327
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/phylogenetic-analyses-and-modelling.pdf
H.O. Minoarivelo, G. Diedericks, C. Hui.Computational Ecology and Software,2015,5(4):328-339
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/forms-and-genesis-of-species-abundance-distributions.pdf
Evans O. Ochiaga, Cang Hui.Computational Ecology and Software,2015,5(4):340-353
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/modelling-spread-with-context-based-dispersal-strategies.pdf
Andriamihaja Ramanantoanina, Cang Hui.Computational Ecology and Software,2015,5(4):354-366
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/modeling-ecology-and-epidemiology.pdf
Min Su, Hong Wang.Computational Ecology and Software,2015,5(4):367-379
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/discrete-homotopy-perturbation-method-for-non-linear-Schrodinger-equation.pdf
H. A. Wahab, Khalid Usman, Muhammad Naeem, Sarfraz Ahmad, Saira Bhatti, Muhammad
Shahzad, Hazrat Ali.Computational Ecology and Software,2015,5(4):380-388
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
http://www.iaees.org/publications/journals/ces/articles/2015-5(4)/method-of-extreme-points.pdf
L.V. Nedorezov.Computational Ecology and Software,2015,5(4):389-401
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.
Evaluating the developmental instability of Scatophagus argus
(Linnaeus, 1766) from Lower Agusan River Basin, Butuan City,
Philippines using fluctuating asymmetry
http://www.iaees.org/publications/journals/ces/articles/2016-6(1)/developmental-instability-of-Scatophagus-argus-using-asymmetry.pdf
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 and Software,2016,6(1):1-11
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
http://www.iaees.org/publications/journals/ces/articles/2016-6(1)/uncertainty-associated-to-the-forecast-of-species-dispersals.pdf
Alessandro Ferrarini.Computational Ecology and Software,2016,6(1):12-20
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
http://www.iaees.org/publications/journals/ces/articles/2016-6(1)/coral-reef-assessment-and-monitoring.pdf
S. R. M. Tabugo, D.L. Manzanares, A.D. Malawani.Computational Ecology and Software,2016,6(1):21-30
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.
Network toxicology: A new science
http://www.iaees.org/publications/journals/ces/articles/2016-6(2)/network-toxicology.pdf
WenJun Zhang.Computational Ecology and Software,2016,6(2):31-40
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)
http://www.iaees.org/publications/journals/ces/articles/2016-6(2)/exact-solutions-of-nonlinear-problems-by-Homotopy-Analysis-Method.pdf
Hafiz Abdul Wahab, Saira Bhatti, Mohammad Naeem.Computational Ecology and Software,2016,6(2):41-54
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
http://www.iaees.org/publications/journals/ces/articles/2016-6(2)/asymmetry-in-evaluating-developmental-instability.pdf
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 and Software,2016,6(2):55-65
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.
Quantification of uncertainty in the reliability of migration between
habitat patches
http://www.iaees.org/publications/journals/ces/articles/2016-6(3)/quantification-of-uncertainty-in-reliability-of-migration.pdf
Ali Muhammad Ali Rushdi, Ahmad Kamal Hassan.Computational Ecology and Software,2016,6(3):66-82
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)
http://www.iaees.org/publications/journals/ces/articles/2016-6(3)/mathematical-approach-stress-related-behaviors-in-golden-bellied-capuchins.pdf
J. A. Jamielniak, A.G. Garcia.Computational Ecology and Software,2016,6(3):83-94
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)
http://www.iaees.org/publications/journals/ces/articles/2016-6(3)/relative-warp-analysis-determining-morphological-variation.pdf
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 and Software,2016,6(3):95-105
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
http://www.iaees.org/publications/journals/ces/articles/2016-6(3)/lubrication-approximation-theory-for-blade-coating-process.pdf
Saira Bhatti, M. A. Rana, A. M. Siddiqui, M. Zahid, Hafiz Abdul Wahab.Computational Ecology and Software,2016,6(3):106-119
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.
Describing the body shape variation of spotted barb, Puntius
binotatus (Valenciennes 1842) using fluctuating asymmetry from
Tubay, Agusan del Norte, Philippines
http://www.iaees.org/publications/journals/ces/articles/2016-6(4)/describing-the-body-shape-variation-of-spotted-barb.pdf
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 and Software,2016,6(4):120-129
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
http://www.iaees.org/publications/journals/ces/articles/2016-6(4)/structural-control-of-ecological-and-biological-networks.pdf
Alessandro Ferrarini.Computational Ecology and Software,2016,6(4):130-138
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
http://www.iaees.org/publications/journals/ces/articles/2016-6(4)/application-of-process-based-biogeochemical-model-DNDC.pdf
A Biswal, KK Choudhury, P Venkat Raju, MVR Sesha Sai.Computational Ecology and Software,2016,6(4):139-149
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
http://www.iaees.org/publications/journals/ces/articles/2016-6(4)/load-balancing-in-distributed-framework.pdf
Sheraz Ahmad, Faisal Bahdur, Faiza Kanwal, Riaz Shah.Computational Ecology and Software,2016,6(4):150-164
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.
A new model to describe the relationship between species richness
and sample size
http://www.iaees.org/publications/journals/ces/articles/2017-7(1)/relationship-between-species-richness-and-sample-size.pdf
WenJun Zhang.Computational Ecology and Software,2017,7(1):1-7
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
http://www.iaees.org/publications/journals/ces/articles/2017-7(1)/fluctuating-asymmetry-of-spotted-barb.pdf
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 and Software,2017,7(1):8-27
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
http://www.iaees.org/publications/journals/ces/articles/2017-7(1)/an-approximate-solution-for-a-generalized-Hirota-Satsom-equation.pdf
H.A. Wahab, Rafi Ullah, Saira Bhatti, M. Shahzad, M. Naeem, Fawad Hussain, Sarfraz Ahmad.Computational Ecology and Software,2017,7(1):28-37
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.
MATASS: the software for multi-attribute assessment problems
http://www.iaees.org/publications/journals/ces/articles/2017-7(2)/MATASS-software-for-multi-attribute-assessment-problems.pdf
WenJun Zhang. YanHong Qi, Xin LI.Computational Ecology and Software,2017,7(2):38-48
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
http://www.iaees.org/publications/journals/ces/articles/2017-7(2)/multi-criteria-decision-making-methods-in-GIS.pdf
E. Chamanehpour, Ahmadizadeh, Akbarpour.Computational Ecology and Software,2017,7(2):49-64
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
http://www.iaees.org/publications/journals/ces/articles/2017-7(2)/geometric-morphometric-analysis-describing-sexual-dimorphism-in-wings.pdf
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 and Software,2017,7(2):65-81
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.
Comparative growth models of big-scale sand smelt (Atherina boyeri
Risso, 1810) sampled from Hirfanll Dam Lake, Klrsehir, Ankara, Turkey
http://www.iaees.org/publications/journals/ces/articles/2017-7(2)/comparative-growth-models-of-big-scale-sand-smelt.pdf
S. Benzer, R. Benzer.Computational Ecology and Software,2017,7(2):82-90
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.
Analysis of variance: Comfortless questions
http://www.iaees.org/publications/journals/ces/articles/2017-7(3)/analysis-of-variance-Comfortless-questions.pdf
L.V. Nedorezov.Computational Ecology and Software,2017,7(3):91-99
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
http://www.iaees.org/publications/journals/ces/articles/2017-7(3)/effect-of-automobiles-on-global-warming.pdf
Shyam Sundar, Ashish Kumar Mishra, Ram Naresh.Computational Ecology and Software,2017,7(3):100-108
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
http://www.iaees.org/publications/journals/ces/articles/2017-7(3)/WORMSPREAD-an-individual-based-model-of-invasive-earthworm.pdf
George W. Armstrong, Ahsan Mahmood, Andie Nugent, Sonya Dexter, Emily Hutto, Timothy S.
McCay, Ahmet Ay.Computational Ecology and Software,2017,7(3):109-122
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
http://www.iaees.org/publications/journals/ces/articles/2017-7(3)/shell-shape-variations-and-sexual-dimorphism-of-Snail.pdf
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 and Software,2017,7(3):123-139
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.
Analysis of complex wetland ecological system: Effect of harvesting
http://www.iaees.org/publications/journals/ces/articles/2017-7(4)/analysis-of-complex-wetland-ecological-system.pdf
Nilesh Kumar Thakur, Rashi Gupta.Computational Ecology and Software,2017,7(4):140-152
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
http://www.iaees.org/publications/journals/ces/articles/2017-7(4)/period-doubling-bifurcation-and-chaos-control.pdf
Qamar Din, Muhammad Asif Khan.Computational Ecology and Software,2017,7(4):153-166
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
http://www.iaees.org/publications/journals/ces/articles/2017-7(4)/Elliptic-Fourier-Analysis-of-body-shape-variation.pdf
S. R. M. Tabugo-Rico, L.A. Tumanda, C.K. Cabrido, C.M. Apale, E. Dumalagan.Computational Ecology and Software,2017,7(4):167-178
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
http://www.iaees.org/publications/journals/ces/articles/2017-7(4)/DSSAT-crop-model-for-wheat-crop-growth-simulation.pdf
Anima Biswal, Bhabhana Sahay, KV Ramana, MVR Sesha Sai.Computational Ecology and Software,2017,7(4):179-187
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
http://www.iaees.org/publications/journals/ces/articles/2018-8(1)/dynamic-models-for-development-of-insecticide-resistance.pdf
WenJun Zhang, GuiLu Zhang.Computational Ecology and Software,2018,8(1):1-6
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
http://www.iaees.org/publications/journals/ces/articles/2018-8(1)/mathematical-model-of-mosquito-dynamics.pdf
L.V. Nedorezov, J.J. Yermekbayeva, A.N. Omarov, B.N. Nedorezova.Computational Ecology and Software,2018,8(1):7-14
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
http://www.iaees.org/publications/journals/ces/articles/2018-8(1)/nocturnal-flights-lead-to-collision-risk.pdf
Marco Gustin, Giuseppe Giglio, Stefania C. Pellegrino, Annagrazia Frassanito, Alessandro
Ferrarini.Computational Ecology and Software,2018,8(1):15-22
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
http://www.iaees.org/publications/journals/ces/articles/2018-8(1)/morphotypes-of-cone-snails.pdf
S. R. M. Tabugo, S.R. Boco, S.I.G Masangcay, J.D. Anunciado, C.M.Q. Pao.Computational Ecology and Software,2018,8(1):23-31
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
http://www.iaees.org/publications/journals/ces/articles/2018-8(1)/fuzzy-modeling-for-the-spread-of-influenza-virus.pdf
Renu Verma, S.P. Tiwari, Ranjit Kumar Upadhyay.Computational Ecology and Software,2018,8(1):32-45
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.
Geometric morphometrics of leaf blade shape in water hyacinth
(Eichhornia crassipes: Pontederiaceae) population from Lake Mainit,
Philippines
http://www.iaees.org/publications/journals/ces/articles/2018-8(2)/geometric-morphometrics-of-leaf-blade-shape.pdf
C.C. Cabuga, Jr, I.C.B. Delabahan, J.I.C. Dedel, M.A. Ayaton, L.A. Ombat, M.L.M. Budlayan.Computational Ecology and Software,2018,8(2):46-56
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
http://www.iaees.org/publications/journals/ces/articles/2018-8(2)/finding-maximum-flow-in-the-network.pdf
WenJun Zhang.Computational Ecology and Software,2018,8(2):57-61
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
http://www.iaees.org/publications/journals/ces/articles/2018-8(3)/disparity-in-pronotal-shapes-betweensexes.pdf
D. M. Carillo, I.N. dela Cruz.Computational Ecology and Software,2018,8(3):62-74
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
http://www.iaees.org/publications/journals/ces/articles/2018-8(3)/sustainable-urban-development-using-Ecological-Footprint-Method.pdf
Q. Haghparast, Ahmadizadeh, Javad Dawoudian.Computational Ecology and Software,2018,8(3):75-87
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.
Sexual dimorphism in the carapace of mud crab (Scylla serrate,
Forsskal, 1775) in Magallanes, Agusandel Norte using Geometric
Morphometric Analysis
http://www.iaees.org/publications/journals/ces/articles/2018-8(4)/sexual-dimorphism-in-the-carapace-of-mud-crab.pdf
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 and Software,2018,8(4):88-97
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
http://www.iaees.org/publications/journals/ces/articles/2018-8(4)/relative-warp-analysis-of-wing-shape-variations.pdf
Danilo A. Gualberto, Cesar G. Demayo.Computational Ecology and Software,2018,8(4):98-111
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.
Three different ways for estimating Green Oak Leaf Roller dynamics
type: OLS, MEP, and Almost-Bayesian approaches
http://www.iaees.org/publications/journals/ces/articles/2019-9(1)/estimating-Green-Oak-Leaf-Roller-dynamics-type.pdf
L.V. Nedorezov.Computational Ecology and Software,2019,9(1):1-18
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
http://www.iaees.org/publications/journals/ces/articles/2019-9(1)/crowding-effects-and-depletion-mechanisms-of-population-regulation.pdf
Kumar G. Ranjith, Das Kalyan, K. Lakshminarayan, Reddy B. Ravindra.Computational Ecology and Software,2019,9(1):19-36
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.
Bifurcation analysis and chaos control in a discrete-time predator-prey
system with Crowley-Martin functional response
http://www.iaees.org/publications/journals/ces/articles/2019-9(2)/bifurcation-analysis-and-chaos-control-in-discrete-time-predator-prey-system.pdf
S. M. Sohel Rana.Computational Ecology and Software,2019,9(2):37-57
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
http://www.iaees.org/publications/journals/ces/articles/2019-9(2)/fractal-analysis-of-Hippocampus-spp.pdf
S. R. M. Tabugo, R.C.M. H. Ortega, C. S. Padasas.Computational Ecology and Software,2019,9(2):58-66
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 emergence 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.