coexist (version 1.0)

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

Description

batch analysis to plot matrix values for pairwise parameter matrix

Usage

batch.pdf.pairpar(parmatlist, pagesetup = c(2, 2), path = NULL)

Arguments

parmatlist

a list of data generated from batch.mpaircomp() function

pagesetup

how many plots would print in a page of the pdf document, default is 2*2=4 plots

path

local disk path for saving the pdf graphics, if given, the file name will be changed by adding a postfix as "00yh"+a rand uniform number+".pdf" to avoid re-write another file with the same file name. If not given, the file name would be saved to a default path "c://outcome/" with a postfix "pairwiseparameters"+ a random number+".pdf"

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.

See Also

batch.pdf.onepar, batch.monepar, batch.mpaircomp

Examples

##---- 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 (parmatlist, pagesetup = c(2, 2), path = NULL) 
{
    scenarionum <- length(parmatlist)
    parnum <- length(parmatlist[[1]][[1]])
    if (length(path) != 0) {
        randnum <- runif(1)
        pos <- unlist(gregexpr("/", path))
        folder <- substr(path, 1, pos[length(pos)] - 1)
        dir.create(folder, showWarnings = F)
        filename = paste(path, "00yh", randnum, ".pdf", sep = "")
    }
    else {
        randnum <- runif(1)
        dir.create(folder, showWarnings = F)
        filename = paste(folder, "pairwiseparameters", randnum, 
            ".pdf", sep = "")
    }
    pdf(filename)
    par(mfrow = pagesetup)
    for (each in 1:parnum) {
        for (i in 1:scenarionum) {
            xname = paste("Model", i, sep = "-")
            title = names(parmatlist[[i]][[1]])[each]
            t <- parmatlist[[i]][[1]][[each]]
            t <- t(t)
            make.heatmap(t, xname = xname, xlab = c(0.1, 0.25, 
                0.5, 0.75, 0.9), ylab = c(0.1, 0.25, 0.5, 0.75, 
                0.9), title = title)
        }
    }
    dev.off()
  }