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

View on CRAN

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

Functions

batch.coexistence Man page
batch.mcoexistence Man page
batch.monepar Man page
batch.mpaircomp Man page
batch.n2n Man page
batch.onepar Man page
batch.paircomp Man page
batch.pdf.onepar Man page
batch.pdf.pairpar Man page
batch.read Man page
coexist Man page
coexist-package Man page
comblist Man page
comblist2 Man page
competition Man page
compvar Man page
convert.filenames Man page
dispersal Man page
dispvar Man page
fast.flexsim Man page
filename.check Man page
flex.competition Man page
flex.dispersal Man page
flexsim Man page
make.heatmap Man page
make.parcomb Man page
parsetting Man page
plot_n2n Man page
read.data Man page
read.patchdata Man page
sim.coarse Man page
spabundance Man page
sta.coexistence Man page
sta.comparison Man page
sta.fitness Man page
sta.mcoexistence Man page
sta.mcomparison Man page
sta.mpaircomparison Man page
sta.paircomparison Man page

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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