Learn R Programming

coexist (version 1.0)

Species coexistence modeling and analysis

Description

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

Copy Link

Version

Install

install.packages('coexist')

Monthly Downloads

22

Version

1.0

License

GPL (>= 2.0)

Maintainer

Youhua Chen

Last Published

August 2nd, 2012

Functions in coexist (1.0)

batch.onepar

batch analysis to explore coexistence density for handling multiple model scenarios outputs for a varying parameter, for 2-species model
competition

perform competition analysis in the 2-species modeling
comblist2

construct a full list of all combinations of parameters
coexist-package

species coexistence modeling and analysis
batch.coexistence

batch anlaysis of coexistence summary tables
batch.mpaircomp

batch analysis to explore coexistence density for different scenarios of a pair of parameters, for the case of multiple species modeling
batch.paircomp

batch analysis to explore coexistence density for handling different model scenarios for two focused parameters,for 2-species model
spabundance

initialization of species' abundance across the patches/islands
make.heatmap

make a heatmap based on matrix values
read.patchdata

read species abundance data from the patches, an internal function
batch.n2n

batch analysis of niche and neutral/nearly-neutral cases for two or multiple species modeling
batch.pdf.pairpar

batch analysis to plot matrix heatmaps for pairwise parameter matrices for different scenarios and generate pdf graphics
flexsim

species coexistence simulation for multiple-species modeling (>=2)
flex.competition

perform flexible competition analysis allowing multiple species
compvar

competition parameters' matrix
sta.comparison

posterior different parameter rate comparison for a single scenario of 2-species modeling
sta.mpaircomparison

pairwise parameter comparison for multiple species with multiple parameter space
comblist

construct a full list of all combinations of parameters
sta.mcoexistence

basic posterior coexistence analysis for a single scenario of the multiple-species simulation
batch.mcoexistence

batch anlaysis of multiple coexistence summary tables, the batch form for sta.mcoexistence() function
make.parcomb

make the parameter combination index matrix
dispersal

perform dispersal analysis for each simulation time step for 2-species modeling
sta.paircomparison

pairwise parameter comparison for 2-species model
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
batch.read

batch read different file data based on the order 1,2,3,4,5,6... in a folder
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
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
sta.mcomparison

posterior different parameter rate comparison for a single scenario of multiple-species modeling
sim.coarse

2-species coexistence modeling based on the matrix listing out all combinations of parameter setting
flex.dispersal

perform species-specific dispersal and fluctuating source analysis, for two or multiple species models, it's an internal function
filename.check

open,check and create a new folder if not existed
sta.coexistence

posterior coexistence analysis
fast.flexsim

faster multiple species simulation, but just a bit, not fast actually
dispvar

dispersal parameters' matrix
sta.fitness

fitness/abundance comparison for neutral versus niche cases for 2-species modeling
batch.monepar

batch analysis to explore multiple species coexistence density for a varying parameter under multiple-species modeling