[adegenet-commits] r727 - pkg/man www www/files

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

Author: jombart
Date: 2010-11-29 00:21:35 +0100 (Mon, 29 Nov 2010)
New Revision: 727

Added:
   pkg/man/inbreeding.ml.Rd
   www/files/practical-day2.1.1.pdf
Modified:
   www/documentation.html
Log:
added doc file for inbreeding.ml
fixed material for Bogota.


Added: pkg/man/inbreeding.ml.Rd
===================================================================
--- pkg/man/inbreeding.ml.Rd	                        (rev 0)
+++ pkg/man/inbreeding.ml.Rd	2010-11-28 23:21:35 UTC (rev 727)
@@ -0,0 +1,87 @@
+\encoding{UTF-8}
+\name{Inbreeding estimation}
+\alias{inbreeding.ml}
+\title{Likelihood-based estimation of inbreeding}
+\description{
+  The function \code{inbreeding.ml} estimates the inbreeding coefficient
+  of an individuals (F) by computing its likelihood function. It can
+  return either the density of probability of F, or a sample of F values
+  from this distribution. This operation is performed for all the
+  individuals of a \linkS4class{genind} object.
+}
+\usage{
+inbreeding(x, pop = NULL, truenames = TRUE, res.type = c("sample", "function"), N = 200, M = N * 10)
+}
+\arguments{
+  \item{x}{an object of class \linkS4class{genind}.}
+  \item{pop}{a factor giving the 'population' of each individual. If NULL,
+    pop is seeked from \code{pop(x)}. Note that the term population refers in
+    fact to any grouping of individuals'.}
+  \item{truenames}{a logical indicating whether true names should be
+    used (TRUE, default) instead of generic labels (FALSE); used if
+    res.type is "matrix".}
+ \item{res.type}{a character string matching "sample" or "function",
+   specifying whether the output should be a function giving the density of probability
+   of F values ("function") or a sample of F values taken from this
+   distribution ("sample", default).}
+ \item{N}{an integer indicating the size of the sample to be taken from
+   the distribution of F values.}
+ \item{M}{an integer indicating the number of different F values to be
+   used to generate the sample. Values larger than N are recommended to
+   avoid poor sampling of the distribution.}
+}
+\value{
+  A named list with one component for each individual, each of which is
+  a function or a vector of sampled F values (see \code{res.type} argument).
+}
+\seealso{
+  \code{\link{inbreeding}}: a more basic estimator of F with graphical outputs.
+  \code{\link{Hs}}: computation of expected heterozygosity.
+}
+\details{
+  Let \eqn{F} denote the inbreeding coefficient, defined as the
+  probability for an individual to inherit two identical alleles from a
+  single ancestor.
+
+  Let \eqn{p_i} refer to the frequency of allele \eqn{i} in the population. Let
+  \eqn{h} be an variable which equates 1 if the individual is
+  homozygote, and 0 otherwise. For one locus, the probability of being
+  homozygote is computed as:
+
+  \eqn{ F + (1-F) \sum_i p_i^2}
+
+  The probability of being heterozygote is:
+  \eqn{1 - (F + (1-F) \sum_i p_i^2)}
+  
+  The likelihood of a genotype is defined as the probability of being
+  the observed state (homozygote or heterozygote). In the case of
+  multilocus genotypes, log-likelihood are summed over the loci.
+}
+\author{
+  Thibaut Jombart \email{t.jombart at imperial.ac.uk}\cr
+}
+\examples{
+## cattle breed microsatellite data
+data(microbov)
+
+## isolate Lagunaire breed
+lagun <- seppop(microbov)$Lagunaire
+
+## estimate inbreeding - return sample of F values
+Fsamp <- inbreeding.ml(lagun)
+
+## plot the first 10 results
+invisible(sapply(Fsamp[1:10], function(e) plot(density(e), xlab="F", xlim=c(0,1), main="Density of the sampled F values")))
+
+## compute means for all individuals
+Fmean=sapply(Fsamp, mean)
+hist(Fmean, col="orange", xlab="mean value of F", main="Distribution of mean F across individuals")
+
+## estimate inbreeding - return proba density functions
+Fdens <- inbreeding.ml(lagun, res.type="function")
+
+## view function for the first individual
+Fdens[[1]]
+
+## plot the first 10 functions
+invisible(sapply(Fdens[1:10], plot, ylab="Density", main="Density of probability of F values"))

Modified: www/documentation.html
===================================================================
--- www/documentation.html	2010-11-28 23:18:24 UTC (rev 726)
+++ www/documentation.html	2010-11-28 23:21:35 UTC (rev 727)
@@ -38,21 +38,24 @@
 dataset
 reproducing
 AFLP
-data <br>
+data
+<br>
 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &gt; <a href="files/haplo.txt">haplo.txt</a>:
 a
 toy
 dataset
 reproducing
 haploid
-data <br>
+data
+<br>
 &nbsp;&nbsp;&nbsp; &nbsp;&nbsp; &gt; <a href="files/triplo.txt">triplo.txt</a>:
 a
 toy
 dataset
 reproducing
 triploid
-data <br>
+data
+<br>
 - <a href="files/worksOnlyInDiploids.txt">worksOnyInDiploids.txt</a>:
 the list of <span style="font-weight: bold;">functions</span> working <span
  style="font-weight: bold;">only for diploid</span> genotypes <br>
@@ -72,9 +75,10 @@
 2</a>: finding clusters, using cluster information<br>
 &nbsp;&nbsp;&nbsp; &gt; <a href="files/day3.1.2.pdf">lecture 3</a>:
 spatial genetics<br>
-&nbsp;&nbsp;&nbsp; &gt; practical 1 <br>
+&nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day1.1.2.pdf">practical
+1</a> <br>
 &nbsp;&nbsp;&nbsp; &gt;
-<a href="files/practical-day1.1.2.pdf">practical 2 </a><br>
+<a href="files/practical-day2.1.1.pdf">practical 2 </a><br>
 &nbsp;&nbsp;&nbsp; &gt; <a href="files/practical-day3.1.1.pdf">practical
 3</a><br>
 <br>
@@ -86,7 +90,7 @@
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   <a href="http://www.google.fr/"><img
  src="http://www.google.com/logos/Logo_40wht.gif" alt="Google"
- border="0" align="middle"></a><br>
+ align="middle" border="0"></a><br>
   </div>
   <div style="text-align: left;"><input name="q" size="31"
  maxlength="255" value="Enter keywords here" type="text"><!--<INPUT TYPE=hidden name="domains" value="adegenet.r-forge.r-project.org" />--><input

Added: www/files/practical-day2.1.1.pdf
===================================================================
--- www/files/practical-day2.1.1.pdf	                        (rev 0)
+++ www/files/practical-day2.1.1.pdf	2010-11-28 23:21:35 UTC (rev 727)
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[TRUNCATED]

To get the complete diff run:
    svnlook diff /svnroot/adegenet -r 727