Description Usage Arguments Details Author(s) References See Also Examples
read the data from one model/scenario output
1 |
path |
local filename for the model output |
index |
local fielname/path for recording all the paramter combination |
spnum |
species number in the model, default is 2 |
islandnum |
patch number in the model,default is 10 |
return a list of data, for each list member there is a paramater combination item in a vector form and an abundance matrix of species-patches
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 31 32 33 34 35 | ##---- 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 (path = NULL, index = NULL, spnum = 2, islandnum=10)
{
if (is.character(index)) {
indmat <- read.table(index, header = T)
index = indmat
}
if (length(path) != 0) {
raw <- scan(path, what = character(), sep = "\t")
fileline <- length(count.fields(path))
outlist <- list()
length(outlist) <- fileline/(spnum + 1)
sp <- matrix(0, nrow = spnum, ncol = islandnum)
count = 0
for (i in 1:length(raw)) {
if (raw[i] == "V1") {
count = count + 1
for (j in 1:spnum) {
sp[j, ] = as.numeric(raw[(i + 10 + j + (j -
1) * islandnum):(i + 10 + j - 1 + j * islandnum)])
}
par <- index[count, ]
names(par) <- c(paste("r", 1:spnum, sep = ""),
paste("dis", 1:spnum, sep = ""), paste("c",
1:spnum, sep = ""))
outlist[[count]] <- list(abund = sp, pars = par)
}
}
}
return(outlist)
}
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