Description Usage Arguments Value Author(s) References See Also Examples
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).
1 | sta.mcomparison(coexistence, coenum, island, spnum, parameters)
|
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 <=total species number |
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 |
will return a list, each list member is a matrix for one parameter.
Youhua Chen <yhchen@zoology.ubc.ca>
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 | ##---- 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)
}
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