[Adephylo-commits] r182 - in pkg: R man

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

Author: jombart
Date: 2012-09-26 22:49:55 +0200 (Wed, 26 Sep 2012)
New Revision: 182

Added:
   pkg/man/dibas.Rd
Modified:
   pkg/R/dibas.R
Log:
Added doc for dibas.


Modified: pkg/R/dibas.R
===================================================================
--- pkg/R/dibas.R	2012-09-26 18:33:45 UTC (rev 181)
+++ pkg/R/dibas.R	2012-09-26 20:49:55 UTC (rev 182)
@@ -138,7 +138,7 @@
 ###############
 ## dibas.phylo
 ###############
-dibas.phylo <- function(x, grp, method=c("default","leaveOneOut"), metric=c("Abouheif", "nNodes", "sumDD"),...){
+dibas.phylo <- function(x, grp, method=c("default","leaveOneOut"), metric=c("Abouheif", "nNodes", "patristic", "sumDD"),...){
     if(!require(ape)) stop("ape package is required")
     if(!inherits(x,"phylo")) stop("x is not a phylo object")
 

Added: pkg/man/dibas.Rd
===================================================================
--- pkg/man/dibas.Rd	                        (rev 0)
+++ pkg/man/dibas.Rd	2012-09-26 20:49:55 UTC (rev 182)
@@ -0,0 +1,117 @@
+\encoding{UTF-8}
+\name{dibas}
+\alias{dibas}
+\alias{dibas.matrix}
+\alias{dibas.dist}
+\alias{dibas.phylo}
+\alias{simDatGroups}
+\title{DIstance-Based Assignment}
+\description{
+  These functions are under development. Please do not use them unless
+  asked by the author.
+}
+\usage{
+\method{dibas}{phylo}(x, grp, method = c("default", "leaveOneOut"),
+      metric = c("nNodes", "patristic", "Abouheif", "sumDD"), \ldots)
+
+\method{dibas}{matrix}(x, grp, method = c("default", "leaveOneOut"), ldots)
+
+\method{dibas}{dist}(x, grp, method = c("default", "leaveOneOut"), \ldots)
+
+}
+\arguments{
+  \item{x}{a \code{phylo} object, or a symmetric matrix of pairwise distances
+    of class \code{matrix} or \code{dist}.}
+  \item{grp}{a \code{factor} indicating the groups of observations.}
+  \item{method}{a character string indicating the method to be used for
+    estimating the distribution of pairwise distances within
+    groups. The default method ("default") uses all observations, while
+    the "leaveOneOut" estimates separate group distributions for each
+    individual, leaving this one out in the estimation process.}
+  \item{metric}{a character string matching "nNodes", "patristic", "Abouheif", or
+    "sumDD" indicating the distance measure to be used. See
+    \code{\link{distTips}} for more information. Note that patristic
+    distances should be avoided in presence of one or more highly
+    diverse group because of the 'hand fan' syndrome (see example).}
+  \item{\dots}{further arguments passed to other methods. Can be used to
+    provide arguments to \code{\link{table.phylo4d}} in \code{plot} method.}
+}
+\author{ Thibaut Jombart \email{tjombart at imperial.ac.uk} }
+\examples{
+if(require(ape)){
+#### SIMPLE SIMULATED DATA ####
+## 50 variables, 2 groups, 30 indiv
+dat <- simDatGroups(k=2, p=50, n=c(15,15), mu=c(0,1))
+names(dat)
+
+## make a tree
+tre <- nj(dist(dat$dat))
+plot(tre,type="unr", tip.col=c("blue","red")[as.integer(dat$grp)],main="simulated data - tree")
+ 
+## use dibas method
+res <- dibas(tre, dat$grp, metric="nNodes")
+res
+
+barplot(t(res$prob), main="group membership probabilities")
+
+
+
+#### NON-PARAMETRIC TEST BASED ON MEAN SUCCESSFUL ASSIGNMENT ####
+## use dibas method
+distHo <- replicate(100, dibas(tre, sample(dat$grp), metric="patristic")$mean.ok)
+pval <- mean(res$mean.ok<=c(distHo,res$mean.ok))
+pval
+
+hist(c(distHo,res$mean.ok), col="grey", main="Mean successful assignement - permuted values")
+abline(v=res$mean.ok, col="red")
+mtext(side=3, text="Observed value in red")
+
+
+
+#### HAND FAN SYNDROME ####
+## 50 variables, 2 groups, 30 indiv
+dat <- simDatGroups(k=2, p=50, n=c(15,15), mu=c(0,1), sigma=c(2,4))
+names(dat)
+
+## make a tree
+tre <- nj(dist(dat$dat))
+plot(tre,type="unr", tip.col=c("blue","red")[as.integer(dat$grp)],main="simulated data - tree")
+
+## use dibas method
+res <- dibas(tre, dat$grp, metric="nNodes")
+res$grp.tab # results OK
+
+res.patri <- dibas(tre, dat$grp, metric="patristic")
+res.patri$grp.tab # poor results
+
+
+
+
+
+#### MORE COMPLEX DATASET ####
+if(require(adegenet)){
+
+dat <- simDatGroups(k=5, p=50, n=c(5,10,10,30,60), mu=1:5, sigma=sample(1:5)/2)
+names(dat)
+
+## make a tree
+tre <- nj(dist(dat$dat))
+plot(tre,type="unr", tip.col=fac2col(dat$grp),main="simulated data - tree")
+
+## use dibas method
+res <- dibas(tre, dat$grp, metric="Abouheif")
+res
+
+}
+
+}
+
+
+
+
+
+
+
+
+}
+\keyword{multivariate}
\ No newline at end of file