[adegenet-commits] r626 - in pkg: R man

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

Author: jombart
Date: 2010-05-11 11:54:14 +0200 (Tue, 11 May 2010)
New Revision: 626

Modified:
   pkg/R/haploGen.R
   pkg/man/haploGen.Rd
Log:
documenting haploGen.


Modified: pkg/R/haploGen.R
===================================================================
--- pkg/R/haploGen.R	2010-05-11 08:24:58 UTC (rev 625)
+++ pkg/R/haploGen.R	2010-05-11 09:54:14 UTC (rev 626)
@@ -394,7 +394,7 @@
 #####################
 ## seqTrack.haploGen
 #####################
-seqTrack.haploGen <- function(x, optim=c("min","max"), prox.mat=NULL, ...){
+seqTrack.haploGen <- function(x, best=c("min","max"), prox.mat=NULL, ...){
     myX <- dist.dna(x$seq, model="raw")
     x.names <- labels(x)
     x.dates <- as.POSIXct(x)
@@ -406,7 +406,7 @@
     } else {
         mu0 <- eval(prevCall$mu)
     }
-    res <- seqTrack(myX, x.names=x.names, x.dates=x.dates, optim=optim, prox.mat=prox.mat,...)
+    res <- seqTrack(myX, x.names=x.names, x.dates=x.dates, best=best, prox.mat=prox.mat,...)
     return(res)
 }
 

Modified: pkg/man/haploGen.Rd
===================================================================
--- pkg/man/haploGen.Rd	2010-05-11 08:24:58 UTC (rev 625)
+++ pkg/man/haploGen.Rd	2010-05-11 09:54:14 UTC (rev 626)
@@ -19,10 +19,51 @@
   review. They will be documented once accepted for publication.
   Please email the author if you are interested in using it.
 }
-% \usage{
+\usage{
+haploGen(seq.length=1000, mu=0.0001, t.max=50,
+                     gen.time=function(){round(rnorm(1,5,1))},
+                     repro=function(){round(rnorm(1,2,1))}, max.nb.haplo=1e3,
+                     geo.sim=TRUE, grid.size=5, lambda.xy=0.5,
+                     mat.connect=NULL,
+                     ini.n=1, ini.xy=NULL)
 
-% }
-% \arguments{
-%   % \item{}{}
-% }
+print.haploGen(x, ...)
+
+"[.haploGen"(x,i,j,drop=FALSE)
+
+labels.haploGen(object, ...)
+
+as.POSIXct.haploGen(x, tz="", origin=as.POSIXct("2000/01/01"), ...)
+
+seqTrack.haploGen(x, best=c("min","max"), prox.mat=NULL, ...)
+
+as.seqTrack.haploGen(x)
+
+plotHaploGen(x, annot=FALSE, date.range=NULL, col=NULL, bg="grey", add=FALSE, ...)
+
+sample.haploGen(x, n)
+
+setAs("haploGen", "graphNEL", def=function(from)
+
+}
+\arguments{
+  \item{seq.length}{}
+  \item{mu}{}
+  \item{t.max}{}
+  \item{gen.time}{}
+  \item{repro}{}
+  \item{max.nb.haplo}{}
+  \item{geo.sim}{}
+  \item{grid.size}{}
+  \item{lambda.xy}{}
+  \item{mat.connect}{}
+  \item{ini.n}{}
+  \item{ini.xy}{}
+  \item{x,object}{}
+  \item{i,j}{}
+  \item{best}{}
+  \item{prox.mat}{}
+  \item{annot,date.range,col,bg,add}{}
+  \item{n}{}
+ }
 \author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}