read.data: read data with paramter combination index file
In coexist: Species coexistence modeling and analysis

Description Usage Arguments Details Author(s) References See Also Examples

read the data from one model/scenario output

1	read.data(path = NULL, index = NULL, spnum = 2, islandnum=10)

`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.

batch.read, read.patchdata

##---- 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)
  }