[Adephylo-commits] r124 - in pkg: R man

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

Author: jombart
Date: 2009-11-05 11:50:58 +0100 (Thu, 05 Nov 2009)
New Revision: 124

Modified:
   pkg/R/abouheif.R
   pkg/R/ppca.R
   pkg/R/table.phylo4d.R
   pkg/man/maples.Rd
   pkg/man/orthogram.Rd
Log:
- fixed \item in doc
- fixed calls to tdata


Modified: pkg/R/abouheif.R
===================================================================
--- pkg/R/abouheif.R	2009-11-05 10:26:12 UTC (rev 123)
+++ pkg/R/abouheif.R	2009-11-05 10:50:58 UTC (rev 124)
@@ -27,7 +27,7 @@
     if(inherits(x, "phylo4d")){
         if (is.character(chk <- checkPhylo4(x))) stop("bad phylo4d object: ",chk)
         ## if (is.character(chk <- checkData(x))) stop("bad phylo4d object: ",chk) : no longer needed
-        x <- tdata(x)
+        x <- tdata(x, type="tip")
     }
 
     ## main computations

Modified: pkg/R/ppca.R
===================================================================
--- pkg/R/ppca.R	2009-11-05 10:26:12 UTC (rev 123)
+++ pkg/R/ppca.R	2009-11-05 10:50:58 UTC (rev 124)
@@ -32,7 +32,7 @@
     N <- nTips(x)
 
     ## data matrix X
-    X <- tdata(x, which="tip")
+    X <- tdata(x, type="tip")
     X.colnames <- names(X)
     X.rownames <- row.names(X)
     temp <- sapply(X, is.numeric)

Modified: pkg/R/table.phylo4d.R
===================================================================
--- pkg/R/table.phylo4d.R	2009-11-05 10:26:12 UTC (rev 123)
+++ pkg/R/table.phylo4d.R	2009-11-05 10:50:58 UTC (rev 124)
@@ -30,7 +30,7 @@
     tre <- suppressWarnings(as(x,"phylo"))
     ##tre$node.label <- x at node.label # this should be done by the as(x,"phylo")
     ## plot only tree if no tip data
-    if(ncol(tdata(x,which="tip")) == 0) {
+    if(ncol(tdata(x,type="tip")) == 0) {
         plot.phylo(tre, type=treetype, direction="rightwards", show.tip.label=show.tip.label,
                    show.node.label=show.node.label, cex=cex.label,
                    no.margin=FALSE, x.lim=NULL, y.lim=NULL, ...)
@@ -39,7 +39,7 @@
 
 #### data handling
     ## retrieve data
-    dat <- tdata(x, which="tip")
+    dat <- tdata(x, type="tip")
     dat <- dat[, repVar, drop=FALSE]
     clas <- lapply(dat,class)
     isNum <- sapply(clas, function(e) e %in% c("integer","numeric"))

Modified: pkg/man/maples.Rd
===================================================================
--- pkg/man/maples.Rd	2009-11-05 10:26:12 UTC (rev 123)
+++ pkg/man/maples.Rd	2009-11-05 10:50:58 UTC (rev 124)
@@ -8,8 +8,8 @@
 \usage{data(maples)}
 \format{
 \code{tithonia} is a list containing the 2 following objects :  
-            \item{tre}{is a character string giving the phylogenetic tree in Newick format.} 
-            \item{tab}{is a data frame with 17 species and 31 traits}    
+            - tre: a character string giving the phylogenetic tree in Newick format.\cr
+            - tab: a data frame with 17 species and 31 traits}\cr
 }
 \source{
 Data were obtained from the URL

Modified: pkg/man/orthogram.Rd
===================================================================
--- pkg/man/orthogram.Rd	2009-11-05 10:26:12 UTC (rev 123)
+++ pkg/man/orthogram.Rd	2009-11-05 10:50:58 UTC (rev 124)
@@ -46,11 +46,11 @@
 The function computes the variance decomposition of a quantitative vector x on an orthonormal basis B. The variable is normalized given the uniform weight to eliminate problem of scales.
 It plots the squared correlations \eqn{R^{2}}{R^2} between x and vectors of B (variance decomposition) and the cumulated squared correlations \eqn{SR^{2}}{SR^2} (cumulative decomposition).
 The function also provides five non parametric tests to test the existence of autocorrelation. The tests derive from the five following statistics :
-    \item{R2Max}{=\eqn{\max(R^{2})}{max(R^2)}. It takes high value when a high part of the variability is explained by one score.}
-    \item{SkR2k}{=\eqn{\sum_{i=1}^{n-1}(iR^{2}_i)}{sum_i^(n-1) i*(R^2)_i}. It compares the part of variance explained by internal nodes to the one explained by end nodes.}
-    \item{Dmax}{=\eqn{\max_{m=1,...,n-1}(\sum_{j=1}^{m}R^{2}_j - \frac{m}{n-1})}{max_(m=1,...,n-1)(sum_(j=1)^m(R^2_j) - (m/n-1))}. It examines the accumulation of variance for a sequence of scores.}
-    \item{SCE}{=\eqn{\sum_{m=1}^{n-1} (\sum_{j=1}^{m}R^{2}_j - \frac{m}{n-1})^{2}}{sum_(m=1)^(n-1)(sum_(j=1)^m(R^2_j) - (m/n-1))^2}. It examines also the accumulation of variance for a sequence of scores.}
-    \item{ratio}{depends of the parameter posinega. If posinega > 0, the statistic ratio exists and equals \eqn{\sum_{i=1}^{posinega}R^{2}_i}{sum_i (R^2)_i with i < posinega + 1}. It compares the part of variance explained by internal nodes to the one explained by end nodes when we can define how many vectors correspond to internal nodes.}
+    - R2Max=\eqn{\max(R^{2})}{max(R^2)}. It takes high value when a high part of the variability is explained by one score.\cr
+    - SkR2k=\eqn{\sum_{i=1}^{n-1}(iR^{2}_i)}{sum_i^(n-1) i*(R^2)_i}. It compares the part of variance explained by internal nodes to the one explained by end nodes.\cr
+    - Dmax=\eqn{\max_{m=1,...,n-1}(\sum_{j=1}^{m}R^{2}_j - \frac{m}{n-1})}{max_(m=1,...,n-1)(sum_(j=1)^m(R^2_j) - (m/n-1))}. It examines the accumulation of variance for a sequence of scores.\cr
+    - SCE=\eqn{\sum_{m=1}^{n-1} (\sum_{j=1}^{m}R^{2}_j - \frac{m}{n-1})^{2}}{sum_(m=1)^(n-1)(sum_(j=1)^m(R^2_j) - (m/n-1))^2}. It examines also the accumulation of variance for a sequence of scores.\cr
+    - ratio: depends of the parameter posinega. If posinega > 0, the statistic ratio exists and equals \eqn{\sum_{i=1}^{posinega}R^{2}_i}{sum_i (R^2)_i with i < posinega + 1}. It compares the part of variance explained by internal nodes to the one explained by end nodes when we can define how many vectors correspond to internal nodes.
 }
 \value{
 If (high.scores = 0), returns an object of class \code{'krandtest'} (randomization tests) corresponding to the five non parametric tests. \cr \cr