coexist: Species coexistence modeling and analysis
Version 1.0

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

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AuthorYouhua Chen
Date of publication2012-08-02 09:32:01
MaintainerYouhua Chen <yhchen@zoology.ubc.ca>
LicenseGPL (>= 2.0)
Version1.0
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("coexist")

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

Files

DESCRIPTION
MD5
man
man/spabundance.Rd
man/batch.monepar.Rd
man/competition.Rd
man/sim.coarse.Rd
man/batch.pdf.pairpar.Rd
man/plot_n2n.Rd
man/sta.mcomparison.Rd
man/sta.mpaircomparison.Rd
man/comblist.Rd
man/batch.onepar.Rd
man/filename.check.Rd
man/sta.paircomparison.Rd
man/batch.n2n.Rd
man/batch.coexistence.Rd
man/batch.mcoexistence.Rd
man/parsetting.Rd
man/flex.competition.Rd
man/read.data.Rd
man/comblist2.Rd
man/sta.coexistence.Rd
man/read.patchdata.Rd
man/batch.pdf.onepar.Rd
man/sta.mcoexistence.Rd
man/batch.read.Rd
man/make.parcomb.Rd
man/dispersal.Rd
man/batch.paircomp.Rd
man/flex.dispersal.Rd
man/sta.fitness.Rd
man/coexist-package.Rd
man/make.heatmap.Rd
man/batch.mpaircomp.Rd
man/fast.flexsim.Rd
man/compvar.Rd
man/flexsim.Rd
man/sta.comparison.Rd
man/dispvar.Rd
man/convert.filenames.Rd
NAMESPACE
R
R/coexist.R
coexist documentation built on May 20, 2017, 2:22 a.m.