[Picante-commits] r50 - / pkg pkg/R pkg/man

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

Author: skembel
Date: 2008-04-11 08:31:34 +0200 (Fri, 11 Apr 2008)
New Revision: 50

Modified:
   TODO
   pkg/DESCRIPTION
   pkg/R/comm.phylo.cor.R
   pkg/man/comm.phylo.cor.Rd
   pkg/man/picante-package.Rd
Log:
Misc updates to TODO, package description help, comm phylo functions and help

Modified: TODO
===================================================================
--- TODO	2008-04-11 06:13:22 UTC (rev 49)
+++ TODO	2008-04-11 06:31:34 UTC (rev 50)
@@ -6,12 +6,13 @@
 ====
 For 0.1
 -------
--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
--add data files for example purposes (phylocom sample, traits, phylo)
--improve documentation especially for ses.mpd, ses.mnnd, phylosignal, ?
+-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 ses.mpd/ses.mnnd
+-merge community structure and phylocom functions into one file?
+-improve documentation to pass R check
 
-For 0.2
+
+For 0.2 and beyond
 -------
 -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

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2008-04-11 06:13:22 UTC (rev 49)
+++ pkg/DESCRIPTION	2008-04-11 06:31:34 UTC (rev 50)
@@ -1,8 +1,8 @@
 Package: picante
 Type: Package
 Title: Tools for integrating phylogenies and ecology
-Version: 0.1
-Date: 2008-2-22
+Version: 0.1-1
+Date: 2008-4-16
 Author: Steve Kembel <skembel at berkeley.edu>, David Ackerly <dackerly at berkeley.edu>, Simon Blomberg <s.blomberg1 at uq.edu.au>, Peter Cowan <pdc at berkeley.edu>, Cam Webb <cwebb at oeb.harvard.edu>
 Maintainer: Steve Kembel <skembel at berkeley.edu>
 Depends: ape, vegan

Modified: pkg/R/comm.phylo.cor.R
===================================================================
--- pkg/R/comm.phylo.cor.R	2008-04-11 06:13:22 UTC (rev 49)
+++ pkg/R/comm.phylo.cor.R	2008-04-11 06:31:34 UTC (rev 50)
@@ -8,8 +8,8 @@
 	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 <- phylo.dist(sample.prune(samp,phylo))
-	pool.phylo.dist <- phylo.dist(phylo)
+	phylo.dist <- as.dist(cophenetic(sample.prune(samp,phylo)))
+	pool.phylo.dist <- as.dist(cophenetic(phylo))
 	taxa.names <- rownames(as.matrix(phylo.dist))
 	samp.dist <- species.dist(samp,metric)
 	results$obs.corr <- cor(phylo.dist,samp.dist,use="pairwise")

Modified: pkg/man/comm.phylo.cor.Rd
===================================================================
--- pkg/man/comm.phylo.cor.Rd	2008-04-11 06:13:22 UTC (rev 49)
+++ pkg/man/comm.phylo.cor.Rd	2008-04-11 06:31:34 UTC (rev 50)
@@ -6,7 +6,10 @@
   Calculates measures of community phylogenetic structure (correlation between co-occurrence and phylogenetic distance) under various null models
 }
 \usage{
-comm.phylo.cor(samp, phylo, metric = c("cij", "jaccard", "roij"), null.model = c("sample.taxa.labels", "pool.taxa.labels", "keepFreq", "keepRichness", "weighted.sample.pool"), runs = 99)
+comm.phylo.cor(samp, phylo, metric = c("cij", "checkerboard","jaccard", "roij"),
+    null.model = c("sample.taxa.labels", "pool.taxa.labels","frequency", "richness",
+    "weighted.sample.pool"), runs = 99)
+
 }
 \arguments{
   \item{samp}{ Community data matrix }
@@ -16,8 +19,12 @@
   \item{runs}{ Number of runs (randomizations) }
 }
 \value{
-  \item{obs.cor }{Observed correlation}
-  \item{etc }{todo}
+  \item{obs.corr }{Observed co-occurrence/phylogenetic distance correlation}
+    obs.corr.p
+    obs.rank
+    runs = runs
+    obs.rand.p
+    random.corrs = vector(length = runs)    
   ...
 }
 \references{ Cavender-Bares et al. 2004, 2006 }

Modified: pkg/man/picante-package.Rd
===================================================================
--- pkg/man/picante-package.Rd	2008-04-11 06:13:22 UTC (rev 49)
+++ pkg/man/picante-package.Rd	2008-04-11 06:31:34 UTC (rev 50)
@@ -12,14 +12,14 @@
 \tabular{ll}{
 Package: \tab picante\cr
 Type: \tab Package\cr
-Version: \tab 0.1\cr
-Date: \tab 2007-12-05\cr
+Version: \tab 0.1-1\cr
+Date: \tab 2008-04-16\cr
 License: \tab GPL v2\cr
 }
 More details forthcoming
 }
 \author{
-Steve Kembel <skembel at berkeley.edu>, David Ackerly <dackerly at berkeley.edu>, Simon Blomberg <s.blomberg1 at uq.edu.au>, Cam Webb <cwebb at oeb.harvard.edu>
+Steve Kembel <skembel at berkeley.edu>, David Ackerly <dackerly at berkeley.edu>, Simon Blomberg <s.blomberg1 at uq.edu.au>, Peter Cowan <pdc at berkeley.edu>, Cam Webb <cwebb at oeb.harvard.edu>
 
 Maintainer: Steve Kembel <skembel at berkeley.edu>
 }