[Vegan-commits] r2009 - pkg/vegan/R

[noreply at r-forge.r-project.org]

Author: jarioksa
Date: 2011-11-19 07:54:26 +0100 (Sat, 19 Nov 2011)
New Revision: 2009

Added:
   pkg/vegan/R/rarecurve.R
Log:
add rarecurve: draw rarefaction curves for each data row

Added: pkg/vegan/R/rarecurve.R
===================================================================
--- pkg/vegan/R/rarecurve.R	                        (rev 0)
+++ pkg/vegan/R/rarecurve.R	2011-11-19 06:54:26 UTC (rev 2009)
@@ -0,0 +1,37 @@
+`rarecurve` <-
+    function(x, step = 1, sample, xlab = "Sample Size", ylab = "Species",
+             label = TRUE,...)
+{
+    tot <- rowSums(x)
+    S <- specnumber(x)
+    nr <- nrow(x)
+    ## Rarefy
+    out <- lapply(seq_len(nr), function(i) {
+        n <- seq(1, tot[i], by = step)
+        if (n[length(n)] != tot[i])
+            n <- c(n, tot[i])
+        drop(rarefy(x[i,], n))
+    })
+    Nmax <- sapply(out, function(x) max(attr(x, "Subsample")))
+    Smax <- sapply(out, max)
+    ## set up plot
+    plot(c(1, max(Nmax)), c(1, max(Smax)), xlab = xlab, ylab = ylab,
+         type = "n", ...)
+    ## rarefied richnesses for given 'sample'
+    if (!missing(sample)) {
+        abline(v = sample)
+        rare <- sapply(out, function(z) approx(x = attr(z, "Subsample"), y = z,
+                                             xout = sample, rule = 1)$y)
+        abline(h = rare, lwd=0.5)
+    }
+    ## rarefaction curves
+    for(ln in seq_len(length(out))) {
+        N <- attr(out[[ln]], "Subsample")
+        lines(N, out[[ln]], ...)
+    }
+    ## label curves at their endpoitns
+    if (label) {
+        ordilabel(cbind(tot, S), labels=rownames(x), ...)
+    }
+    invisible(out)
+}