coexist: Species coexistence modeling and analysis

species coexistence modeling under asymmetric dispersal and fluctuating source-sink dynamics;testing the proportion of coexistence scenarios driven by neutral and niche processes

AuthorYouhua Chen
Date of publication2012-08-02 09:32:01
MaintainerYouhua Chen <yhchen@zoology.ubc.ca>
LicenseGPL (>= 2.0)
Version1.0

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Man pages

batch.coexistence: batch anlaysis of coexistence summary tables

batch.mcoexistence: batch anlaysis of multiple coexistence summary tables, the...

batch.monepar: batch analysis to explore multiple species coexistence...

batch.mpaircomp: batch analysis to explore coexistence density for different...

batch.n2n: batch analysis of niche and neutral/nearly-neutral cases for...

batch.onepar: batch analysis to explore coexistence density for handling...

batch.paircomp: batch analysis to explore coexistence density for handling...

batch.pdf.onepar: batch mode to plot matrix heatmap graphics for different...

batch.pdf.pairpar: batch analysis to plot matrix heatmaps for pairwise parameter...

batch.read: batch read different file data based on the order...

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...

dispersal: perform dispersal analysis for each simulation time step for...

dispvar: dispersal parameters' matrix

fast.flexsim: faster multiple species simulation, but just a bit, not fast...

filename.check: open,check and create a new folder if not existed

flex.competition: perform flexible competition analysis allowing multiple...

flex.dispersal: perform species-specific dispersal and fluctuating source...

flexsim: species coexistence simulation for multiple-species modeling...

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...

plot_n2n: plot distribution of niche and neutral coexistence patterns...

read.data: read data with paramter combination index file

read.patchdata: read species abundance data from the patches, an internal...

sim.coarse: 2-species coexistence modeling based on the matrix listing...

spabundance: initialization of species' abundance across the...

sta.coexistence: posterior coexistence analysis

sta.comparison: posterior different parameter rate comparison for a single...

sta.fitness: fitness/abundance comparison for neutral versus niche cases...

sta.mcoexistence: basic posterior coexistence analysis for a single scenario of...

sta.mcomparison: posterior different parameter rate comparison for a single...

sta.mpaircomparison: pairwise parameter comparison for multiple species with...

sta.paircomparison: pairwise parameter comparison for 2-species model

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