coexist (version 1.0)

plot_n2n: plot distribution of niche and neutral coexistence patterns and generate pdf graphics

Description

make barplots to compare the model outcomes under niche and nearly-neutrality parameter settings

Usage

plot_n2n(resultlist, island, pagesetup = c(1, 1), path = NULL)

Arguments

resultlist

output from batch.n2n() function

island

number of patches in the model

pagesetup

how many figures will be generated in one page

path

local disk filename for saving the pdf graphics; if path==NULL, a random filename will be generated under "c://outcome" folder

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.n2n, batch.coexistence, batch.mcoexistence

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 (resultlist, island = island, pagesetup = c(1, 1), path = NULL) 
{
    prop <- list()
    length(prop) <- length(resultlist)
    scenarionum <- length(resultlist)
    temp <- matrix(0, ncol = 2, nrow = island - 1)
    for (i in 1:scenarionum) {
        temp[, 1] = rev(resultlist[[i]][1:9, 1]/resultlist[[i]][island, 
            1])
        temp[, 2] = rev(resultlist[[i]][1:9, 2]/resultlist[[i]][island, 
            2])
        prop[[i]] <- temp
    }
    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, ".dat", sep = "")
    }
    else {
        randnum <- runif(1)
        dir.create(folder, showWarnings = F)
        filename = paste(folder, "n2nbarplot", randnum, ".dat", 
            sep = "")
    }
    pdf(filename)
    par(mfrow = pagesetup)
    for (i in 1:scenarionum) {
        nnplot <- barplot(prop[[i]], beside = T, axisnames = F, 
            col = 1)
        y <- max(prop[[i]])
        text(nnplot[5, 1], y - 0.05, "Neutrality", font = 2, 
            cex = 2)
        text(nnplot[5, 2], y - 0.05, "Niche", font = 2, cex = 2)
        axis(1, at = nnplot[, 1], labels = c(1, 2, 3, 4, 5, 6, 
            7, 8, 9))
        axis(1, at = nnplot[, 2], labels = c(1, 2, 3, 4, 5, 6, 
            7, 8, 9))
        mtext(paste("Model", i, sep = "-"))
    }
    dev.off()
  }