Species coexistence modeling and analysis

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Documentation for package ‘coexist’ version 1.0

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coexist-package species coexistence modeling and analysis
batch.coexistence batch anlaysis of coexistence summary tables
batch.mcoexistence batch anlaysis of multiple coexistence summary tables, the batch form for sta.mcoexistence() function
batch.monepar batch analysis to explore multiple species coexistence density for a varying parameter under multiple-species modeling
batch.mpaircomp batch analysis to explore coexistence density for different scenarios of a pair of parameters, for the case of multiple species modeling
batch.n2n batch analysis of niche and neutral/nearly-neutral cases for two or multiple species modeling
batch.onepar batch analysis to explore coexistence density for handling multiple model scenarios outputs for a varying parameter, for 2-species model
batch.paircomp batch analysis to explore coexistence density for handling different model scenarios for two focused parameters,for 2-species model
batch.pdf.onepar batch mode to plot matrix heatmap graphics for different model scenarios but only working on the sampling points of one parameter (x-axis) and generate pdf graphics
batch.pdf.pairpar batch analysis to plot matrix heatmaps for pairwise parameter matrices for different scenarios and generate pdf graphics
batch.read batch read different file data based on the order 1,2,3,4,5,6... in a folder
coexist species coexistence modeling and analysis
comblist construct a full list of all combinations of parameters
comblist2 construct a full list of all combinations of parameters
competition perform competition analysis in the 2-species modeling
compvar competition parameters' matrix
convert.filenames convert saved data sets' names in to a vector based on the order of numbers, which will be called by batch.read() function
dispersal perform dispersal analysis for each simulation time step for 2-species modeling
dispvar dispersal parameters' matrix
fast.flexsim faster multiple species simulation, but just a bit, not fast actually
filename.check open,check and create a new folder if not existed
flex.competition perform flexible competition analysis allowing multiple species
flex.dispersal perform species-specific dispersal and fluctuating source analysis, for two or multiple species models, it's an internal function
flexsim species coexistence simulation for multiple-species modeling (>=2)
make.heatmap make a heatmap based on matrix values
make.parcomb make the parameter combination index matrix
parsetting rate vector for each species at each island, called widely by other functions
plot_n2n plot distribution of niche and neutral coexistence patterns and generate pdf graphics
read.data read data with paramter combination index file
read.patchdata read species abundance data from the patches, an internal function
sim.coarse 2-species coexistence modeling based on the matrix listing out all combinations of parameter setting
spabundance initialization of species' abundance across the patches/islands
sta.coexistence posterior coexistence analysis
sta.comparison posterior different parameter rate comparison for a single scenario of 2-species modeling
sta.fitness fitness/abundance comparison for neutral versus niche cases for 2-species modeling
sta.mcoexistence basic posterior coexistence analysis for a single scenario of the multiple-species simulation
sta.mcomparison posterior different parameter rate comparison for a single scenario of multiple-species modeling
sta.mpaircomparison pairwise parameter comparison for multiple species with multiple parameter space
sta.paircomparison pairwise parameter comparison for 2-species model