[adegenet-commits] r390 - pkg/R

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

Author: jombart
Date: 2009-06-10 13:28:41 +0200 (Wed, 10 Jun 2009)
New Revision: 390

Modified:
   pkg/R/haploSim.R
   pkg/R/seqTrack.R
Log:
renaming proxMat -> prox.mat


Modified: pkg/R/haploSim.R
===================================================================
--- pkg/R/haploSim.R	2009-06-10 10:59:13 UTC (rev 389)
+++ pkg/R/haploSim.R	2009-06-10 11:28:41 UTC (rev 390)
@@ -363,7 +363,7 @@
 #####################
 ## seqTrack.haploSim
 #####################
-seqTrack.haploSim <- function(x, optim=c("min","max"), proxMat=NULL, ...){
+seqTrack.haploSim <- function(x, optim=c("min","max"), prox.mat=NULL, ...){
     myX <- dist.dna(x$seq, model="raw")
     seq.names <- labels(x)
     seq.dates <- as.POSIXct(x)
@@ -374,7 +374,7 @@
     } else {
         mu0 <- eval(prevCall$mu)
     }
-    res <- seqTrack(myX, seq.names=seq.names, seq.dates=seq.dates, optim=optim, proxMat=proxMat,...)
+    res <- seqTrack(myX, seq.names=seq.names, seq.dates=seq.dates, optim=optim, prox.mat=prox.mat,...)
     return(res)
 }
 

Modified: pkg/R/seqTrack.R
===================================================================
--- pkg/R/seqTrack.R	2009-06-10 10:59:13 UTC (rev 389)
+++ pkg/R/seqTrack.R	2009-06-10 11:28:41 UTC (rev 390)
@@ -16,7 +16,7 @@
 ## seqTrack
 #############
 seqTrack.default <- function(x, seq.names, seq.dates, optim=c("min","max"),
-                     proxMat=NULL, ...){
+                     prox.mat=NULL, ...){
 
     ## CHECKS ##
     optim <- match.arg(optim)
@@ -41,8 +41,8 @@
 
     x <- as.matrix(x)
 
-    if(!is.null(proxMat) && !identical(dim(proxMat),dim(x))) {
-        stop("proxMat is provided but its dimensions are inconsistent with that of x")
+    if(!is.null(prox.mat) && !identical(dim(prox.mat),dim(x))) {
+        stop("prox.mat is provided but its dimensions are inconsistent with that of x")
     }
 
     N <- length(seq.names)
@@ -53,8 +53,8 @@
     x <- as.matrix(x)
     ## rename dimensions using id
     colnames(x) <- rownames(x) <- id
-    if(!is.null(proxMat)){
-        colnames(proxMat) <- rownames(proxMat) <- id
+    if(!is.null(prox.mat)){
+        colnames(prox.mat) <- rownames(prox.mat) <- id
     }
 
     if(length(seq.names) != nrow(x)){
@@ -79,9 +79,9 @@
 
     ## select among different possible ancestors
     selAmongAncestors <- function(idx,ances){
-        ## Choose the most otherwise connected ancestor, given proxMat
-        if(!is.null(proxMat)){ # if we've got no other info
-            toKeep <- test.equal(max(proxMat[idx,ances]), proxMat[idx,ances])
+        ## Choose the most otherwise connected ancestor, given prox.mat
+        if(!is.null(prox.mat)){ # if we've got no other info
+            toKeep <- test.equal(max(prox.mat[idx,ances]), prox.mat[idx,ances])
             ances <- ances[toKeep]
         }