[Picante-commits] r236 - in pkg: inst/doc man

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

Author: skembel
Date: 2012-09-04 19:21:41 +0200 (Tue, 04 Sep 2012)
New Revision: 236

Modified:
   pkg/inst/doc/picante-intro.Rnw
   pkg/inst/doc/picante-intro.pdf
   pkg/man/comm.phylo.qr.Rd
   pkg/man/pblm.Rd
   pkg/man/pcd.Rd
   pkg/man/pglmm.Rd
   pkg/man/traitgram.Rd
Log:
Modifying vignette and changing several examples to not run in order to meet CRAN check requirements

Modified: pkg/inst/doc/picante-intro.Rnw
===================================================================
--- pkg/inst/doc/picante-intro.Rnw	2012-09-04 01:29:56 UTC (rev 235)
+++ pkg/inst/doc/picante-intro.Rnw	2012-09-04 17:21:41 UTC (rev 236)
@@ -12,7 +12,7 @@
 \date{April 2010}
 
 \begin{document}
-\SweaveOpts{strip.white=TRUE}
+\SweaveOpts{strip.white=true}
 <<echo=FALSE>>=
 options(width=72)
 @
@@ -177,7 +177,6 @@
 <<fig=TRUE>>=
 comdist.result <- comdist(comm, phydist)
 comdist.result
-library(cluster)
 comdist.clusters <- hclust(comdist.result)
 plot(comdist.clusters)
 @

Modified: pkg/inst/doc/picante-intro.pdf
===================================================================
(Binary files differ)

Modified: pkg/man/comm.phylo.qr.Rd
===================================================================
--- pkg/man/comm.phylo.qr.Rd	2012-09-04 01:29:56 UTC (rev 235)
+++ pkg/man/comm.phylo.qr.Rd	2012-09-04 17:21:41 UTC (rev 236)
@@ -51,5 +51,5 @@
 \seealso{ \code{\link{randomizeMatrix}} }
 \examples{
 data(phylocom)
-comm.phylo.qr(phylocom$sample, phylocom$phylo, metric="cij",null.model="sample.taxa.labels")}
+comm.phylo.qr(phylocom$sample, phylocom$phylo, metric="cij", null.model="sample.taxa.labels", runs=99)}
 \keyword{univar}

Modified: pkg/man/pblm.Rd
===================================================================
--- pkg/man/pblm.Rd	2012-09-04 01:29:56 UTC (rev 235)
+++ pkg/man/pblm.Rd	2012-09-04 17:21:41 UTC (rev 236)
@@ -75,6 +75,7 @@
 
 \author{ Matthew Helmus \email{mrhelmus at gmail.com} }
 \examples{
+\dontrun{
 #load example data from Ives & Godfray (2006)
 data(IvesGodfray)
 
@@ -103,6 +104,6 @@
 pblm.A <- pblm(sqrt(A),tree1=host.cov.scaled,tree2=para.cov.scaled)
 pblm.A$signal.strength    #compare to Ives and Godfray (2006) Table 1 Line 1
 pblm.A$MSE
-
 }
+}
 \keyword{univar}
\ No newline at end of file

Modified: pkg/man/pcd.Rd
===================================================================
--- pkg/man/pcd.Rd	2012-09-04 01:29:56 UTC (rev 235)
+++ pkg/man/pcd.Rd	2012-09-04 17:21:41 UTC (rev 236)
@@ -43,7 +43,9 @@
 The sampling procedure used to standardize \emph{PCD} and produce \code{PSVmncd} and \code{PSVpool} can be slow.
 }
 \examples{
+\dontrun{
 data(phylocom)
 pcd(phylocom$sample, phylocom$phylo)
 }
+}
 \keyword{univar}

Modified: pkg/man/pglmm.Rd
===================================================================
--- pkg/man/pglmm.Rd	2012-09-04 01:29:56 UTC (rev 235)
+++ pkg/man/pglmm.Rd	2012-09-04 17:21:41 UTC (rev 236)
@@ -79,7 +79,7 @@
 especially when designing complicated model structures. See Ives and Helmus (2011) for a discussion.
 }
 \examples{
-
+\dontrun{
 modelflag=1
 sim.dat<-pglmm.sim(stree(16, "balanced"),nsites=30,modelflag=modelflag,second.env=TRUE,compscale=1)
 str(sim.dat)
@@ -92,5 +92,6 @@
 str(out)
 out$s # The first row gives the estimate of phylogenetic signal and the second an estimate of how strongly species richness varies across communities. This later parameter is likely biologically uninformative for most research questions.
 }
+}
 
 \keyword{univar}

Modified: pkg/man/traitgram.Rd
===================================================================
--- pkg/man/traitgram.Rd	2012-09-04 01:29:56 UTC (rev 235)
+++ pkg/man/traitgram.Rd	2012-09-04 17:21:41 UTC (rev 236)
@@ -28,7 +28,7 @@
 \references{ 
 Ackerly, D. D. 2009. Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal. Proceedings of the National Academy of Sciences USA 106:19699-19706. doi: 10.1073/pnas.0901635106. 
 
-Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. Climate, Niche Evolution, and Diversification of the \"bird-cage\" Evening Primroses (Oenothera, Sections Anogra and Kleinia). American Naturalist 173:225-240. 
+Evans, M. E. K., S. A. Smith, R. S. Flynn, and M. J. Donoghue. 2009. Climate, Niche Evolution, and Diversification of the "bird-cage" Evening Primroses (Oenothera, Sections Anogra and Kleinia). American Naturalist 173:225-240. 
 }
 \examples{
 randtree <- rcoal(20)