[adegenet-commits] r650 - pkg/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jul 14 11:48:16 CEST 2010
Author: jombart
Date: 2010-07-14 11:48:16 +0200 (Wed, 14 Jul 2010)
New Revision: 650
Modified:
pkg/man/haploGen.Rd
Log:
Can't find the error in the doc...
Modified: pkg/man/haploGen.Rd
===================================================================
--- pkg/man/haploGen.Rd 2010-07-14 09:30:43 UTC (rev 649)
+++ pkg/man/haploGen.Rd 2010-07-14 09:48:16 UTC (rev 650)
@@ -13,6 +13,7 @@
\alias{sample.haploGen}
%\alias{as,haploGen,graphNEL-method}
\alias{coerce,haploGen,graphNEL-method}
+\alias{as,haploGen,graphNEL-method}
\title{Simulation of genealogies of haplotypes}
\description{
The function \code{haploGen} implements simulations of genealogies of
@@ -39,124 +40,118 @@
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)
-
-\method{print}{haploGen}(x, \dots)
-
-\method{"["}{haploGen}(x, i, j, drop=FALSE)
-
+% \method{print}{haploGen}(x, \dots)
+% \method{"["}{haploGen}(x, i, j, drop=FALSE)
\method{labels}{haploGen}(object, \dots)
-
\method{as.POSIXct}{haploGen}(x, tz="", origin=as.POSIXct("2000/01/01"), \dots)
-
\method{seqTrack}{haploGen}(x, best=c("min","max"), prox.mat=NULL, \dots)
-
as.seqTrack.haploGen(x)
-
plotHaploGen(x, annot=FALSE, date.range=NULL, col=NULL, bg="grey", add=FALSE, \dots)
-
sample.haploGen(x, n)
-
-\S4method{coerce}{haploGen,graphNEL}(from, to)
+\S4method{coerce}{haploGen,graphNEL}(from, to, strict=TRUE)
}
\arguments{
\item{seq.length}{an integer indicating the length of the simulated
-haplotypes, in number of nucleotides.}
+ haplotypes, in number of nucleotides.}
\item{mu}{the mutation rate, in number of mutation per site and per
-time unit. Can be a (fixed) number or a function returning a number
-(then called for each replication event).}
+ time unit. Can be a (fixed) number or a function returning a number
+ (then called for each replication event).}
\item{t.max}{an integer indicating the maximum number of time units to
- run the simulation for.}
+ run the simulation for.}
\item{gen.time}{an integer indicating the generation time, in number
-of time units. Can be a (fixed) number or a function returning a number
-(then called for each reproduction event).}
+ of time units. Can be a (fixed) number or a function returning a number
+ (then called for each reproduction event).}
\item{repro}{an integer indicating the number of descendents per
-haplotype. Can be a (fixed) number or a function returning a number
-(then called for each reproduction event).}
+ haplotype. Can be a (fixed) number or a function returning a number
+ (then called for each reproduction event).}
\item{max.nb.haplo}{an integer indicating the maximum number of
-haplotypes handled at any time of the simulation, used to control the
-size of the produced object. Larger number will lead to slower
-simulations. If this number is exceeded, the genealogy is prunded to as
-to keep this number of haplotypes.}
+ haplotypes handled at any time of the simulation, used to control the
+ size of the produced object. Larger number will lead to slower
+ simulations. If this number is exceeded, the genealogy is prunded to as
+ to keep this number of haplotypes.}
\item{geo.sim}{a logical stating whether simulations should be
-spatially explicit (TRUE, default) or not (FALSE). Spatially-explicit
-simulations are slightly slower than their non-spatial counterpart.}
+ spatially explicit (TRUE, default) or not (FALSE). Spatially-explicit
+ simulations are slightly slower than their non-spatial counterpart.}
\item{grid.size}{the size of the square grid of possible locations for
-spatial simulations. The total number of locations will be this number
-squared.}
+ spatial simulations. The total number of locations will be this number
+ squared.}
\item{lambda.xy}{the parameter of the Poisson distribution used to
-determine dispersion in x and y axes.}
+ determine dispersion in x and y axes.}
\item{mat.connect}{a matrix of connectivity describing migration
-amongts all pairs of locations. \code{mat.connect[i,j]} indicates the
-probability, being in 'i', to migrate to 'j'. The rows of this matrix
-thus sum to 1. It has as many rows and columns as there are locations,
-with row 'i' / column 'j' corresponding to locations number 'i' and 'j'.
-Locations are numbered as in a matrix in which rows and columns are
-respectively x and y coordinates. For instance, in a 5x5 grid, locations
-are numbered as in \code{matrix(1:25,5,5)}.
-}
+ amongts all pairs of locations. \code{mat.connect[i,j]} indicates the
+ probability, being in 'i', to migrate to 'j'. The rows of this matrix
+ thus sum to 1. It has as many rows and columns as there are locations,
+ with row 'i' / column 'j' corresponding to locations number 'i' and 'j'.
+ Locations are numbered as in a matrix in which rows and columns are
+ respectively x and y coordinates. For instance, in a 5x5 grid, locations
+ are numbered as in \code{matrix(1:25,5,5)}.
+ }
\item{ini.n}{an integer specifying the number of (identical)
-haplotypes to initiate the simulation}
+ haplotypes to initiate the simulation}
\item{ini.xy}{a vector of two integers giving the x/y coordinates of the initial haplotype.}
\item{x,object}{\code{haploGen} objects.}
\item{i,j, drop}{\code{i} is a vector used for subsetting the object. For
-instance, \code{i=1:3} will retain only the first three haplotypes of the
-genealogy. \code{j} and \code{drop} are only provided for compatibility,
-but not used.}
+ instance, \code{i=1:3} will retain only the first three haplotypes of the
+ genealogy. \code{j} and \code{drop} are only provided for compatibility,
+ but not used.}
\item{best, prox.mat}{arguments to be passed to the
-\code{\link{seqTrack}} function. See documentation of
-\code{\link{seqTrack}} for more information.}
+ \code{\link{seqTrack}} function. See documentation of
+ \code{\link{seqTrack}} for more information.}
\item{annot,date.range,col,bg,add}{arguments to be passed to \code{\link{plotSeqTrack}}.}
\item{n}{an integer indicating the number of haplotypes to be retained
-in the sample}
+ in the sample}
\item{from, to}{arguments of the conversion function, for converting a
-\code{haploGen} object into a \linkS4class{graphNEL}.}
-\item{tz, origin}{ aguments to be passed to \code{\link{as.POSIXct}}
-(see ?as.POSIXct)}
-\item{\dots}{further arguments to be passed to other methods}
- }
+ \code{haploGen} object into a \linkS4class{graphNEL}.}
+ \item{tz, origin}{ aguments to be passed to \code{\link{as.POSIXct}}
+ (see ?as.POSIXct)}
+ \item{\dots}{further arguments to be passed to other methods}
+ \item{strict}{a logical used for compatibility with \code{as} generic
+ function, but not used in the conversion. See \code{\link{setAs}} for
+ more information.}
+}
\author{Thibaut Jombart \email{t.jombart at imperial.ac.uk}}
\references{
-Jombart T, Eggo R, Dodd P, Balloux F (accepted) Reconstructing disease
-outbreaks from genetic data: a graph approach. Heredity.
+ Jombart T, Eggo R, Dodd P, Balloux F (accepted) Reconstructing disease
+ outbreaks from genetic data: a graph approach. Heredity.
}
\value{
-=== haploGen class ===\cr
-\code{haploGen} objects are lists containing the following slots:\cr
-- seq: DNA sequences in the DNAbin matrix format\cr
-- dates: dates of appearance of the haplotypes\cr
-- ances: a vector of integers giving the index of each haplotype's
-ancestor\cr
-- id: a vector of integers giving the index of each haplotype\cr
-- xy: (optional) a matrix of spatial coordinates of haplotypes\cr
-- call: the matched call
+ === haploGen class ===\cr
+ \code{haploGen} objects are lists containing the following slots:\cr
+ - seq: DNA sequences in the DNAbin matrix format\cr
+ - dates: dates of appearance of the haplotypes\cr
+ - ances: a vector of integers giving the index of each haplotype's
+ ancestor\cr
+ - id: a vector of integers giving the index of each haplotype\cr
+ - xy: (optional) a matrix of spatial coordinates of haplotypes\cr
+ - call: the matched call
-=== misc functions ===\cr
-- as.POSIXct: returns a vector of dates with POSIXct format\cr
-- labels: returns the labels of the haplotypes\cr
-- as.seqTrack: returns a seqTrack object. Note that this object is not a
-proper seqTrack analysis, but just a format conversion convenient for
-plotting \code{haploGen} objects.
+ === misc functions ===\cr
+ - as.POSIXct: returns a vector of dates with POSIXct format\cr
+ - labels: returns the labels of the haplotypes\cr
+ - as.seqTrack: returns a seqTrack object. Note that this object is not a
+ proper seqTrack analysis, but just a format conversion convenient for
+ plotting \code{haploGen} objects.
}
\details{
-=== Dependencies with other packages ===\cr
-- ape package is required as it implements efficient handling of DNA
-sequences used in \code{haploGen} objects. To install this package,
-simply type:\cr
-\code{install.packages("ape")}
+ === Dependencies with other packages ===\cr
+ - ape package is required as it implements efficient handling of DNA
+ sequences used in \code{haploGen} objects. To install this package,
+ simply type:\cr
+ \code{install.packages("ape")}
-- for various purposes including plotting, converting genealogies to
-graphs (\linkS4class{graphNEL} class) can be useful. This requires the
-packages graph, and possibly Rgraphviz for plotting. These packages are
-not on CRAN, but on Bioconductor. To install them, use:\cr
-source("http://bioconductor.org/biocLite.R")\cr
-biocLite("graph")\cr
-biocLite("Rgraphviz")
+ - for various purposes including plotting, converting genealogies to
+ graphs (\linkS4class{graphNEL} class) can be useful. This requires the
+ packages graph, and possibly Rgraphviz for plotting. These packages are
+ not on CRAN, but on Bioconductor. To install them, use:\cr
+ source("http://bioconductor.org/biocLite.R")\cr
+ biocLite("graph")\cr
+ biocLite("Rgraphviz")
-See the respective vignettes for more information on using these packages.
+ See the respective vignettes for more information on using these packages.
- === Converting haploGen objects to graphs ===\cr
+ === Converting haploGen objects to graphs ===\cr
\code{haploGen} objects can be converted to \linkS4class{graphNEL}
objects, which can in turn be plotted and manipulated using classical
graph tools. Simply use 'as(x, "graphNEL")' where 'x' is a
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