[Phylobase-commits] r814 - in pkg: . R inst/doc man src
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Oct 27 17:57:15 CEST 2010
Author: bbolker
Date: 2010-10-27 17:57:14 +0200 (Wed, 27 Oct 2010)
New Revision: 814
Modified:
pkg/DESCRIPTION
pkg/R/class-oldclasses.R
pkg/R/readNCL.R
pkg/R/setAs-Methods.R
pkg/inst/doc/developer.pdf
pkg/inst/doc/phylobase.Rnw
pkg/inst/doc/phylobase.pdf
pkg/man/as-methods.Rd
pkg/man/phylo4-display.Rd
pkg/man/phylobase-package.Rd
pkg/man/phylog.Rd
pkg/src/GetNCL.cpp
Log:
ade4 to adephylo switch
docType{method} to docType{methods}
fix typo 'ncll' for 'ncl' in GetNCL.cpp
second attempt at catching NCL exceptions properly
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2010-10-27 13:53:13 UTC (rev 813)
+++ pkg/DESCRIPTION 2010-10-27 15:57:14 UTC (rev 814)
@@ -4,7 +4,7 @@
Version: 0.6.1
Date: 2010-08-06
Depends: methods, grid, ape(>= 2.1), Rcpp (>= 0.8.3)
-Suggests: ade4, MASS
+Suggests: adephylo, MASS
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler, Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara, Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Ben Bolker <bolker at mcmaster.ca>
Description: Provides a base S4 class for comparative methods, incorporating one or more trees and trait data
Modified: pkg/R/class-oldclasses.R
===================================================================
--- pkg/R/class-oldclasses.R 2010-10-27 13:53:13 UTC (rev 813)
+++ pkg/R/class-oldclasses.R 2010-10-27 15:57:14 UTC (rev 814)
@@ -9,5 +9,5 @@
## setOldClass("multi.tree") ## obsolete
-## ade4 classes
+## adephylo classes
setOldClass("phylog")
Modified: pkg/R/readNCL.R
===================================================================
--- pkg/R/readNCL.R 2010-10-27 13:53:13 UTC (rev 813)
+++ pkg/R/readNCL.R 2010-10-27 15:57:14 UTC (rev 814)
@@ -166,7 +166,7 @@
edgeMat <- cbind(ncl$parentVector, c(1:length(ncl$parentVector)))
edgeLgth <- ncl$branchLengthVector
edgeLgth[edgeLgth == -1] <- NA
- if (length(ncl$taxaNames) != min(ncll$parentVector)-1) {
+ if (length(ncl$taxaNames) != min(ncl$parentVector)-1) {
stop("phylobase doesn't deal with multiple taxa block at this time.")
}
## TODO: code node labels in GetNCL
Modified: pkg/R/setAs-Methods.R
===================================================================
--- pkg/R/setAs-Methods.R 2010-10-27 13:53:13 UTC (rev 813)
+++ pkg/R/setAs-Methods.R 2010-10-27 15:57:14 UTC (rev 814)
@@ -170,10 +170,10 @@
})
#######################################################
-## Exporting to ade4
+## Exporting to adephylo
setAs("phylo4", "phylog", function(from, to) {
- if (!require(ade4))
- stop("the ade4 package is required")
+ if (!require(adephylo))
+ stop("the adephylo package is required")
x <- as(from, "phylo")
xstring <- write.tree(x, file = "")
newick2phylog(xstring)
Modified: pkg/inst/doc/developer.pdf
===================================================================
--- pkg/inst/doc/developer.pdf 2010-10-27 13:53:13 UTC (rev 813)
+++ pkg/inst/doc/developer.pdf 2010-10-27 15:57:14 UTC (rev 814)
@@ -160,21 +160,25 @@
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[TRUNCATED]
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svnlook diff /svnroot/phylobase -r 814
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