sta.mcomparison: posterior different parameter rate comparison for a single scenario of multiple-species modeling

Description

Analyze and compare the number of patches that allowed different coexistence cases (for example 2 species coexistence, 3 species coexistence and so on) for the sampling points of the focused parameter (while partialling out the influence of other parameters by taking average).

Usage

sta.mcomparison(coexistence, coenum, island, spnum, parameters)

Arguments

coexistence

The output from sta.mcoexistence() function,which is a matrix, of columns from left to right are the countings of patch numbers that only allowed the survival of a single species (each of the total species number), then followed by the countings of patches that allowed the coexistence of 2 species, 3 species,... until the column that all the species can coexist. After these columns, the others are values for each parameter combination.

coenum

coexisting species number in a patch you want to explore. Should be >=2 and

island

number of patches in the model

spnum

number of species in the model

parameters

a vector for showing sampling points for a parameter, for example c(.2,.5,.9), indicating three sampling points in a single parameter

Value

will return a list, each list member is a matrix for one parameter.

References

Chen YH (2012) coexist: an R package for performing species coexistence modeling and analysis under asymmetric dispersal and fluctuating source-sink dynamics. http://code.google.com/p/coexist.

Examples

Run this code

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (coexistence, coenum, island, spnum, parameters = parspace) 
{
    comparisonlist <- list()
    length(comparisonlist) <- dim(coexistence)[2] - 2 * spnum
    conum <- matrix(0, ncol = length(parameters) + 1, nrow = island)
    colnames(conum) <- c("coe.num", paste("=", parameters, sep = ""))
    for (pars in 1:length(comparisonlist)) {
        for (i in 1:(island - 1)) {
            conum[i, 1] = island - i
            for (j in 1:length(parameters)) {
                conum[i, j + 1] <- length(which(coexistence[, 
                  spnum + coenum] == island - i & coexistence[, 
                  pars + 2 * spnum] == parameters[j]))
            }
        }
        for (j in 1:length(parameters)) {
            conum[island, j + 1] = length(which(coexistence[, 
                spnum + coenum] == parameters[j]))
        }
        comparisonlist[[pars]] <- conum
    }
    names(comparisonlist) <- colnames(coexistence[, (2 * spnum + 
        1):dim(coexistence)[2]])
    return(comparisonlist)
  }