R/accumcomp.R

In BiodiversityR: Package for Community Ecology and Suitability Analysis

`accumcomp` <-
function(x, y="", factor, scale="", method="exact", permutations=100, conditioned=T, gamma="boot",
    plotit=T, labelit=T, legend=T, rainbow=T, xlim=c(1,max), ylim=c(0,rich), type="p",
    xlab="sites", ylab="species richness", cex.lab=1, cex.axis=1, ...) 
{
    groups <- table(y[,factor])
    min <- min(groups)
    max <- max(groups)
    m <- length(groups)
    levels <- names(groups)
    result <- array(NA,dim=c(m,max,3))
    dimnames(result) <- list(level=levels, obs=c(1:max), c("Sites","Richness","sd"))
    names(dimnames(result)) <- c(factor,"obs","")
    for (i in 1:m) {
        result1 <- accumresult(x, y, factor, level=levels[i], scale=scale, method=method, permutations=permutations, conditioned=conditioned, gamma=gamma)
        l <- length(result1$sites)
        result[i,c(1:l),1] <- result1$sites
        result[i,c(1:l),2] <- result1$richness
        if (method!="collector" && method!="poisson" && method!="binomial" && method!="negbinomial") {result[i,c(1:l),3] <- result1$sd}
    }
    if (plotit == T) {
        max <- max(result[,,1],na.rm=T)
        rich <- max(result[,,2],na.rm=T)
        for (i in 1:m) {
            result1 <- accumresult(x, y, factor, level=levels[i], scale=scale, method=method, permutations=permutations, conditioned=conditioned, gamma=gamma)
            if (plotit == T) {
                if (i == 1) {addit <- F}
                if (i > 1) {addit <- T}
                if (labelit==T) {
                    labels <- levels[i]
                }else{
                    labels <- ""
                }
                if (rainbow==T) {
                    grDevices::palette(colorspace::rainbow_hcl(m, c=90, l=50))
                    accumplot(result1, addit=addit, xlab=xlab, ylab=ylab, xlim=xlim, ylim=ylim, labels=labels,
                        col=i, pch=i, type=type, cex.lab=cex.lab, cex.axis=cex.axis,...)
                }else{
                    accumplot(result1, addit=addit, xlab=xlab, ylab=ylab, xlim=xlim, ylim=ylim, labels=labels, pch=i, type=type,...)
                }
            }
        }
        if (rainbow==T && legend==T) {legend(graphics::locator(1), legend=levels, pch=c(1:m), col=c(1:m))}
        if (rainbow==F && legend==T) {legend(graphics::locator(1), legend=levels, pch=c(1:m))}
    }
    grDevices::palette("default")
    return(result)
}