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-package         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
