[Picante-commits] r44 - / pkg pkg/data pkg/man

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

Author: skembel
Date: 2008-03-25 19:41:34 +0100 (Tue, 25 Mar 2008)
New Revision: 44

Added:
   pkg/data/
   pkg/data/phylocom.rda
   pkg/man/phylocom.Rd
Modified:
   TODO
Log:
Added phylocom data for testing

Modified: TODO
===================================================================
--- TODO	2008-03-25 18:14:45 UTC (rev 43)
+++ TODO	2008-03-25 18:41:34 UTC (rev 44)
@@ -6,14 +6,14 @@
 ====
 For 0.1
 -------
--fix trait data input - currently most functions expect a vector with names, should handle/check lack of names and warn
--clean up/hide utility functions, merge into one file/documentation
+-fix trait data input - currently most functions expect a vector with names, should handle/check lack of names and warn. Write helper function.
 -merge community structure and phylocom functions into one file
--reinstate function to call out to phylocom executable and read results back in to R (maybe for 0.2?)
+-add data files for example purposes (phylocom sample, traits, phylo)
 -improve documentation especially for ses.mpd, ses.mnnd, phylosignal, ?
 
 For 0.2
 -------
+-reinstate function to call out to phylocom executable and read results back in to R
 -implement null model heavy lifting in C code - see BB's email for a start
 -allow trait data to be a vector or a data.frame (single or multiple columns)
 -implement contrib index and similar - move to phylobase format?

Added: pkg/data/phylocom.rda
===================================================================
(Binary files differ)


Property changes on: pkg/data/phylocom.rda
___________________________________________________________________
Name: svn:mime-type
   + application/octet-stream

Added: pkg/man/phylocom.Rd
===================================================================
--- pkg/man/phylocom.Rd	                        (rev 0)
+++ pkg/man/phylocom.Rd	2008-03-25 18:41:34 UTC (rev 44)
@@ -0,0 +1,24 @@
+\name{phylocom}
+\alias{phylocom}
+\docType{data}
+\title{ Phylocom default data }
+\description{
+  Tree, community and trait data from the Phylocom 3.41 distribution
+}
+\usage{data(phylocom)}
+\format{
+A list with three elements
+  \item{phylocom$phylo}{Phylogenetic tree}
+  \item{phylocom$sample}{Community data}
+  \item{phylocom$traits}{Trait data}
+}
+
+\source{
+  Webb, C.O., Ackerly, D.D., and Kembel, S.W. 2007. Phylocom: software for the analysis of community phylogenetic structure and trait evolution. Version 3.41. http://www.phylodiversity.net/phylocom/.
+}
+
+\examples{
+data(phylocom)
+ses.mpd(phylocom$sample,cophenetic(phylocom$phylo))
+}
+\keyword{datasets}