[Adephylo-commits] r76 - in pkg: R man

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

Author: jombart
Date: 2008-12-02 20:47:10 +0100 (Tue, 02 Dec 2008)
New Revision: 76

Modified:
   pkg/R/orthogram.R
   pkg/man/orthogram.Rd
   pkg/man/ungulates.Rd
Log:
Fixed some stuff: now package works and passes the check with the orthogram.


Modified: pkg/R/orthogram.R
===================================================================
--- pkg/R/orthogram.R	2008-12-02 17:06:05 UTC (rev 75)
+++ pkg/R/orthogram.R	2008-12-02 19:47:10 UTC (rev 76)
@@ -65,7 +65,7 @@
             stop("missing value in 'x'")
     }
     if(type == "factor"){
-        dudi1 <- dudi.acm(data.frame(x), scannf = F, nf = min(nobs, nlevels(x)))
+        dudi1 <- dudi.acm(data.frame(x), scannf = FALSE, nf = min(nobs, nlevels(x)))
     }
     if(type == "dudi") {
         if (!all.equal(x$lw, rep(1/nobs, nobs)))

Modified: pkg/man/orthogram.Rd
===================================================================
--- pkg/man/orthogram.Rd	2008-12-02 17:06:05 UTC (rev 75)
+++ pkg/man/orthogram.Rd	2008-12-02 19:47:10 UTC (rev 76)
@@ -15,12 +15,10 @@
 \arguments{
   \item{x}{a numeric vector corresponding to the quantitative variable}
   \item{orthobas}{an object of class \code{'orthobasis'}}
-  \item{neig}{an object of class \code{'neig'}}
-  \item{phylog}{an object of class \code{'phylog'}}
+  \item{prox}{a matrix of phylogenetic proximities as returned by \code{\link{proxTips}}.}
   \item{nrepet}{an integer giving the number of permutations}
   \item{posinega}{a parameter for the ratio test. If posinega > 0, the function computes the ratio test.}
   \item{tol}{a tolerance threshold for orthonormality condition}
-  \item{na.action}{if 'fail' stops the execution of the current expression when \code{z} contains any missing value. If 'mean' replaces any missing values by mean(\code{z})}
   \item{cdot}{a character size for points on the cumulative decomposition display}
   \item{cfont.main}{a character size for titles}
   \item{lwd}{a character size for dash lines}
@@ -52,7 +50,7 @@
 }
 \author{
   Original code: Sébastien Ollier and Daniel Chessel.\cr
-  Current maintainer: St\ephane Dray <dray at biomserv.univ-lyon1.fr>
+  Current maintainer: Stéphane Dray <dray at biomserv.univ-lyon1.fr>
 }
 \seealso{
   \code{\link{orthobasis.phylo}}

Modified: pkg/man/ungulates.Rd
===================================================================
--- pkg/man/ungulates.Rd	2008-12-02 17:06:05 UTC (rev 75)
+++ pkg/man/ungulates.Rd	2008-12-02 19:47:10 UTC (rev 76)
@@ -4,7 +4,7 @@
 \docType{data}
 \title{Phylogeny and quantitative traits of ungulates.}
 \description{
-This data set describes the phylogeny of 18 ungulates as reported by P\'elabon et al. (1995). It also gives 4 traits corresponding to these 18 species.
+This data set describes the phylogeny of 18 ungulates as reported by Pélabon et al. (1995). It also gives 4 traits corresponding to these 18 species.
 }
 \usage{data(ungulates)}
 \format{
@@ -22,7 +22,7 @@
   - ls: is a numeric vector that describes the litter size \cr
 }
 \source{
-Data were obtained from P\'elabon, C., Gaillard, J.M., Loison, A. and Portier, A. (1995) 
+Data were obtained from Pélabon, C., Gaillard, J.M., Loison, A. and Portier, A. (1995) 
 Is sex-biased maternal care limited by total maternal expenditure in polygynous ungulates? 
 \emph{Behavioral Ecology and Sociobiology}, \bold{37}, 311--319.
 }