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

Author
Youhua Chen
Date of publication
2012-08-02 09:32:01
Maintainer
Youhua Chen <yhchen@zoology.ubc.ca>
License
GPL (>= 2.0)
Version
1.0

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

Files in this package

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