[Picante-commits] r63 - / pkg/R pkg/man

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

Author: skembel
Date: 2008-04-26 02:28:05 +0200 (Sat, 26 Apr 2008)
New Revision: 63

Modified:
   TODO
   pkg/R/phylodiversity.R
   pkg/R/phylosignal.R
   pkg/man/picante-package.Rd
Log:
Cleaning up wreckage after moving and renaming functions

Modified: TODO
===================================================================
--- TODO	2008-04-26 00:03:39 UTC (rev 62)
+++ TODO	2008-04-26 00:28:05 UTC (rev 63)
@@ -6,10 +6,8 @@
 ====
 For 0.1
 -------
--fix trait data input - currently many functions expect a vector with names, should handle/check lack of names and warn. Write helper function.
--Doublecheck name matching for comm.phylo.cor and mpd/mnnd/ses.mpd/ses.mnnd
--merge community structure and phylocom functions into one file?
 -improve documentation for public release
+-data name checking and matching - currently many functions expect data to have names that match e.g. phylo$tip.labels, should handle/check lack of names and warn. Write helper function.
 
 For 0.2 and beyond
 -------
@@ -18,7 +16,7 @@
 -allow trait data to be a vector or a data.frame (single or multiple columns)
 -implement contrib index and similar
 -move to phylobase format
--qr on comdist as option
+-qr on com.phylo.corr as option
 -trait gradient analysis and contrast diagnostics functions from DDA
 -taxaShuffle and comstruct functions - rewrite to use indices in place of names for efficiency
 -vignettes

Modified: pkg/R/phylodiversity.R
===================================================================
--- pkg/R/phylodiversity.R	2008-04-26 00:03:39 UTC (rev 62)
+++ pkg/R/phylodiversity.R	2008-04-26 00:28:05 UTC (rev 63)
@@ -8,7 +8,7 @@
 	null.model <- match.arg(null.model)
 	results <- list("obs.corr"=NA,"obs.corr.p"=NA,"obs.rank"=NA,"runs"=runs,
 			"obs.rand.p"=NA,"random.corrs"=vector(length=runs))
-	phylo.dist <- as.dist(cophenetic(sample.prune(samp,phylo)))
+	phylo.dist <- as.dist(cophenetic(prune.sample(samp,phylo)))
 	pool.phylo.dist <- as.dist(cophenetic(phylo))
 	taxa.names <- rownames(as.matrix(phylo.dist))
 	samp.dist <- as.dist(as.matrix(species.dist(samp,metric))[taxa.names,taxa.names])

Modified: pkg/R/phylosignal.R
===================================================================
--- pkg/R/phylosignal.R	2008-04-26 00:03:39 UTC (rev 62)
+++ pkg/R/phylosignal.R	2008-04-26 00:28:05 UTC (rev 63)
@@ -57,16 +57,16 @@
 }
 
 'multiPhylosignal' <-
-function(x,tree,...) {
+function(x,phy,...) {
 	trait <- x[,1]
 	names(trait) <- row.names(x)
-	pruned <- pruneMissing(trait,tree)
+	pruned <- prune.missing(trait,phy)
 	output <- data.frame(phylosignal(pruned$data,pruned$tree,...))
 	if(length(colnames(x))>1) {
 		for (i in 2:length(colnames(x))) {
 			trait <- x[,i]
 			names(trait) <- row.names(x)
-			pruned <- pruneMissing(trait,tree)
+			pruned <- prune.missing(trait,phy)
 			output <- rbind(output,phylosignal(pruned$data,pruned$tree,...))
 		}
 	}

Modified: pkg/man/picante-package.Rd
===================================================================
--- pkg/man/picante-package.Rd	2008-04-26 00:03:39 UTC (rev 62)
+++ pkg/man/picante-package.Rd	2008-04-26 00:28:05 UTC (rev 63)
@@ -6,7 +6,7 @@
 Picante: Phylocom Integration, Community Analyses, Null-models, Traits, and Evolution in R
 }
 \description{
-Collection of functions for integrating ecology and evolutionary biology.
+Collection of functions for integrating ecology and evolutionary biology
 }
 \details{
 \tabular{ll}{