[Vegan-commits] r923 - pkg/vegan/R

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

Author: jarioksa
Date: 2009-08-12 22:13:20 +0200 (Wed, 12 Aug 2009)
New Revision: 923

Added:
   pkg/vegan/R/estaccumR.R
Removed:
   pkg/vegan/R/estaccum.R
Log:
renamed estaccum.R to estaccumR.R

Deleted: pkg/vegan/R/estaccum.R
===================================================================
--- pkg/vegan/R/estaccum.R	2009-08-12 20:10:58 UTC (rev 922)
+++ pkg/vegan/R/estaccum.R	2009-08-12 20:13:20 UTC (rev 923)
@@ -1,21 +0,0 @@
-##" Individual based accumulation model. Similar to poolaccum but uses
-##estimateR. Inherits from "poolaccum" class and uses its methods.
-`estaccumR` <-
-    function(x, permutations = 100)
-{
-    n <- nrow(x)
-    N <- seq_len(n)
-    S <- chao <- ace <- matrix(0, nrow = n, ncol = permutations)
-    for (i in 1:permutations) {
-        take <- sample(n)
-        tmp <- estimateR(apply(x[take,], 2, cumsum))
-        S[,i] <- tmp[1,]
-        chao[,i] <- tmp[2,]
-        ace[, i] <- tmp[4,]
-    }
-    means <- cbind(N = N, S = rowMeans(S), Chao = rowMeans(chao),
-                   ACE = rowMeans(ace))
-    out <- list(S = S, chao = chao, ace = ace, N = N, means = means)
-    class(out) <- c("estaccumR", "poolaccum")
-    out
-}

Copied: pkg/vegan/R/estaccumR.R (from rev 922, pkg/vegan/R/estaccum.R)
===================================================================
--- pkg/vegan/R/estaccumR.R	                        (rev 0)
+++ pkg/vegan/R/estaccumR.R	2009-08-12 20:13:20 UTC (rev 923)
@@ -0,0 +1,21 @@
+##" Individual based accumulation model. Similar to poolaccum but uses
+##estimateR. Inherits from "poolaccum" class and uses its methods.
+`estaccumR` <-
+    function(x, permutations = 100)
+{
+    n <- nrow(x)
+    N <- seq_len(n)
+    S <- chao <- ace <- matrix(0, nrow = n, ncol = permutations)
+    for (i in 1:permutations) {
+        take <- sample(n)
+        tmp <- estimateR(apply(x[take,], 2, cumsum))
+        S[,i] <- tmp[1,]
+        chao[,i] <- tmp[2,]
+        ace[, i] <- tmp[4,]
+    }
+    means <- cbind(N = N, S = rowMeans(S), Chao = rowMeans(chao),
+                   ACE = rowMeans(ace))
+    out <- list(S = S, chao = chao, ace = ace, N = N, means = means)
+    class(out) <- c("estaccumR", "poolaccum")
+    out
+}