[Picante-commits] r60 - pkg/R

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

Author: skembel
Date: 2008-04-26 01:47:58 +0200 (Sat, 26 Apr 2008)
New Revision: 60

Added:
   pkg/R/phylocom.R
Removed:
   pkg/R/readsample.R
   pkg/R/sample2matrix.R
   pkg/R/writesample.R
   pkg/R/writetraits.R
Log:
Combine phylocom data read/write functions into a single file

Added: pkg/R/phylocom.R
===================================================================
--- pkg/R/phylocom.R	                        (rev 0)
+++ pkg/R/phylocom.R	2008-04-25 23:47:58 UTC (rev 60)
@@ -0,0 +1,45 @@
+`sample2matrix` <-
+function(x) {
+
+#turns a phylocom-format sample file into a sample X species matrix
+#assumes a phylocom-format sample:
+#no header line data
+#column 1 = plot, column 2 = abundance, column 3 = species
+#to load a phylocom-format file directly, try:
+#sample2matrix(read.delim2(file="FILENAME",header=F))
+	colnames(x) <- c("plot","abund","id")
+    y <- tapply(x$abund, list(x$plot, x$id), sum)
+    y[is.na(y)] <- 0
+    y
+}
+
+
+`readsample` <-
+function (filename = "") {
+    x <- read.table(file = filename, header = FALSE, sep = "\t", col.names = c("plot", 
+        "abund", "id"))
+    sample2matrix(x)
+}
+
+
+`writesample` <-
+function (community, filename = "") {
+    write.table(matrix2sample(community), file = filename, append = FALSE, 
+        sep = "\t", eol = "\n", quote = FALSE, row.names = FALSE, col.names = FALSE)
+}
+
+
+`writetraits` <-
+function (trt, file = "", bin = NULL, sigd = 3) 
+{
+    head = matrix(c("3"), ncol = length(names(trt)), nrow = 1)
+    if (!is.null(bin)) 
+        head[bin] = 0
+    write.table(data.frame("type", head), file = file, sep = "\t", 
+        quote = FALSE, row.names = FALSE, col.names = FALSE)
+    write.table(matrix(c("name", colnames(trt)), nrow = 1), 
+        file = file, sep = "\t", append = TRUE, quote = FALSE, 
+        row.names = FALSE, col.names = FALSE)
+    write.table(signif(trt, sigd), sep = "\t", file = file, append = TRUE, quote = FALSE, 
+        row.names = TRUE, col.names = FALSE)
+}

Deleted: pkg/R/readsample.R
===================================================================
--- pkg/R/readsample.R	2008-04-25 23:42:55 UTC (rev 59)
+++ pkg/R/readsample.R	2008-04-25 23:47:58 UTC (rev 60)
@@ -1,7 +0,0 @@
-`readsample` <-
-function (filename = "") {
-    x <- read.table(file = filename, header = FALSE, sep = "\t", col.names = c("plot", 
-        "abund", "id"))
-    sample2matrix(x)
-}
-

Deleted: pkg/R/sample2matrix.R
===================================================================
--- pkg/R/sample2matrix.R	2008-04-25 23:42:55 UTC (rev 59)
+++ pkg/R/sample2matrix.R	2008-04-25 23:47:58 UTC (rev 60)
@@ -1,15 +0,0 @@
-`sample2matrix` <-
-function(x) {
-
-#turns a phylocom-format sample file into a sample X species matrix
-#assumes a phylocom-format sample:
-#no header line data
-#column 1 = plot, column 2 = abundance, column 3 = species
-#to load a phylocom-format file directly, try:
-#sample2matrix(read.delim2(file="FILENAME",header=F))
-	colnames(x) <- c("plot","abund","id")
-    y <- tapply(x$abund, list(x$plot, x$id), sum)
-    y[is.na(y)] <- 0
-    y
-}
-

Deleted: pkg/R/writesample.R
===================================================================
--- pkg/R/writesample.R	2008-04-25 23:42:55 UTC (rev 59)
+++ pkg/R/writesample.R	2008-04-25 23:47:58 UTC (rev 60)
@@ -1,6 +0,0 @@
-`writesample` <-
-function (community, filename = "") {
-    write.table(matrix2sample(community), file = filename, append = FALSE, 
-        sep = "\t", eol = "\n", quote = FALSE, row.names = FALSE, col.names = FALSE)
-}
-

Deleted: pkg/R/writetraits.R
===================================================================
--- pkg/R/writetraits.R	2008-04-25 23:42:55 UTC (rev 59)
+++ pkg/R/writetraits.R	2008-04-25 23:47:58 UTC (rev 60)
@@ -1,15 +0,0 @@
-`writetraits` <-
-function (trt, file = "", bin = NULL, sigd = 3) 
-{
-    head = matrix(c("3"), ncol = length(names(trt)), nrow = 1)
-    if (!is.null(bin)) 
-        head[bin] = 0
-    write.table(data.frame("type", head), file = file, sep = "\t", 
-        quote = FALSE, row.names = FALSE, col.names = FALSE)
-    write.table(matrix(c("name", colnames(trt)), nrow = 1), 
-        file = file, sep = "\t", append = TRUE, quote = FALSE, 
-        row.names = FALSE, col.names = FALSE)
-    write.table(signif(trt, sigd), sep = "\t", file = file, append = TRUE, quote = FALSE, 
-        row.names = TRUE, col.names = FALSE)
-}
-