[Ecopd-commits] r71 - in branches/single-tree: R man

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

Author: regetz
Date: 2009-11-17 05:18:08 +0100 (Tue, 17 Nov 2009)
New Revision: 71

Modified:
   branches/single-tree/R/utilities.R
   branches/single-tree/man/genera.Rd
Log:
modified genera to work on phylo4com objects; updated documentation


Modified: branches/single-tree/R/utilities.R
===================================================================
--- branches/single-tree/R/utilities.R	2009-11-17 04:08:48 UTC (rev 70)
+++ branches/single-tree/R/utilities.R	2009-11-17 04:18:08 UTC (rev 71)
@@ -110,10 +110,23 @@
   return(phy)
 }
 
+##TODO method-ize this, adding method for phylo4, then calling that
+##method from this more complex phylo4com method
 # genera extractor
-genera <- function(phy) {
-  #From taxa names in tree, remove "_" and species name after
-  gsub("_.*$", "", tipLabels(phy))
+genera <- function(phy, comm) {
+    if (missing(comm)) {
+        comm <- communities(phy)
+    }
+    doNotExist <- !comm %in% communities(phy)
+    if (any(doNotExist)) {
+        stop("one or more communities not found in phy: ",
+            paste(comm[doNotExist], collapse=", "))
+    }
+    # From taxa names in tree, remove "_" and species name after
+    g <- lapply(phy at subtrees[phy at metadata$comms[comm]], function(x)
+        gsub("_.*$", "", tipLabels(x)))
+    names(g) <- comm
+    return(g)
 }
 
 # community labels extractor

Modified: branches/single-tree/man/genera.Rd
===================================================================
--- branches/single-tree/man/genera.Rd	2009-11-17 04:08:48 UTC (rev 70)
+++ branches/single-tree/man/genera.Rd	2009-11-17 04:18:08 UTC (rev 71)
@@ -7,10 +7,11 @@
   nomenclature.
 }
 \usage{
-  genera(phy)
+  genera(phy, comm)
 }
 \arguments{
-  \item{phy}{a \code{phylo4} object (or one that inherits from it)}
+  \item{phy}{a \code{phylo4com} object}
+  \item{comm}{a vector of community labels; if missing, all communities}
 }
 \details{
   This is a simple function that assumes the tip labels of phylogeny
@@ -18,11 +19,13 @@
   whatsoever to check whether this is in fact the case.
 }
 \value{
-  A character vector containing the genus portion of the tip labels,
-  with element names corresponding to the numeric tip node ID.
+  A list of character vectors, one per community, containing the genus
+  portion of the tip labels, with element names corresponding to the
+  numeric tip node ID.
 }
 \author{Jim Regetz (regetz at nceas.ucsb.edu)}
 \examples{
   data(weeds)
-  genera(weeds$A)
+  genera(weeds, "A")
+  genera(weeds)
 }