[Rcolony-commits] r12 - pkg/man

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

Author: jonesor
Date: 2009-04-21 15:07:35 +0200 (Tue, 21 Apr 2009)
New Revision: 12

Added:
   pkg/man/get.interm.data.Rd
Log:
added blank help file for get.interm.data function.

Added: pkg/man/get.interm.data.Rd
===================================================================
--- pkg/man/get.interm.data.Rd	                        (rev 0)
+++ pkg/man/get.interm.data.Rd	2009-04-21 13:07:35 UTC (rev 12)
@@ -0,0 +1,94 @@
+\name{plotsibs}
+\alias{plotsibs}
+%- Also NEED an '\alias' for EACH other topic documented here.
+\title{ ~~function to do ... ~~ }
+\description{
+  ~~ A concise (1-5 lines) description of what the function does. ~~
+}
+\usage{
+plotsibs(colony.object, maintitle = "sibships", prob = 0.8, pairwise = FALSE)
+}
+%- maybe also 'usage' for other objects documented here.
+\arguments{
+  \item{colony.object}{ ~~Describe \code{colony.object} here~~ }
+  \item{maintitle}{ ~~Describe \code{maintitle} here~~ }
+  \item{prob}{ ~~Describe \code{prob} here~~ }
+  \item{pairwise}{ ~~Describe \code{pairwise} here~~ }
+}
+\details{
+  ~~ If necessary, more details than the description above ~~
+}
+\value{
+  ~Describe the value returned
+  If it is a LIST, use
+  \item{comp1 }{Description of 'comp1'}
+  \item{comp2 }{Description of 'comp2'}
+  ...
+}
+\references{ ~put references to the literature/web site here ~ }
+\author{ ~~who you are~~ }
+\note{ ~~further notes~~ 
+
+ ~Make other sections like Warning with \section{Warning }{....} ~
+}
+\seealso{ ~~objects to See Also as \code{\link{help}}, ~~~ }
+\examples{
+##---- Should be DIRECTLY executable !! ----
+##-- ==>  Define data, use random,
+##--	or do  help(data=index)  for the standard data sets.
+
+## The function is currently defined as
+function(colony.object,maintitle="sibships",prob=0.8,pairwise=FALSE){
+	 
+	 #Get full and half sibship data.
+if(pairwise==FALSE){	
+sibs<-colony.object$sibs}else{
+sibs<-colony.object$pairwise.sibs
+sibs$Probability<-rep(1,dim(sibs)[1])}
+
+	
+alloffspring<-colony.object$offspring	
+alloffspring$offspring.numID<-as.numeric(alloffspring$offspring.numID)
+
+	 #Apply the numeric ID to the sibship data.
+	 sibs<-merge(sibs,alloffspring,by.x="OffspringID1",by.y="offspringID",sort=FALSE)
+	 names(sibs)[names(sibs)=="offspring.numID"]<-"OffspringID1.num"
+	 
+	 sibs<-merge(sibs,alloffspring,by.x="OffspringID2",by.y="offspringID",sort=FALSE)
+	 names(sibs)[names(sibs)=="offspring.numID"]<-"OffspringID2.num"
+	 sibs$OffspringID1.num<-as.numeric(sibs$OffspringID1.num)
+	 sibs$OffspringID2.num<-as.numeric(sibs$OffspringID2.num)
+	 
+	 
+	 #Set up the plot area.
+	 plot(sibs$OffspringID1.num,sibs$OffspringID2.num,type="n",axes=FALSE,xlab="Offspring X",ylab="Offspring Y")
+	 axis(1,at=alloffspring$offspring.numID,labels=alloffspring$offspringID,las=2)
+	 axis(2,at=alloffspring$offspring.numID,labels=alloffspring$offspringID,las=2)
+	 
+	 polygon(c(0,1.05*max(alloffspring$offspring.numID),1.05*max(alloffspring$offspring.numID)),c(0,0,1.05*max(alloffspring$offspring.numID)),col="#FF669930",border=NA)
+	 polygon(c(0,0,1.05*max(alloffspring$offspring.numID)),c(0,1.05*max(alloffspring$offspring.numID),1.05*max(alloffspring$offspring.numID)),col="#33CCFF30",border=NA)
+	 
+	 legend("topleft","Full Sib",bty="n")
+	 legend("bottomright","Half Sib",bty="n")
+	 
+	 title(main=maintitle)
+	 
+	 #Plot the data.
+	 hs<-subset(sibs,type=="Half"&Probability>prob)
+	 for (i in 1:dim(hs)[1]){
+		 #If Halfsib, then put the greater number first
+		 if(hs[i,5]>hs[i,6]){points(hs[i,5],hs[i,6],pch=16,col="#33CCFF98")}else{points(hs[i,6],hs[i,5],pch=16,col="#33CCFF98")}
+		 }
+	 
+	 fs<-subset(sibs,type=="Full"&Probability>prob)
+	 for (i in 1:dim(fs)[1]){
+		 #If Halfsib, then put the greater number first
+		 if(fs[i,5]<fs[i,6]){points(fs[i,5],fs[i,6],pch=16,col="#FF669998")}else{points(fs[i,6],fs[i,5],pch=16,col="#FF669998")}
+		 }
+	 
+	 }
+}
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{ ~kwd1 }
+\keyword{ ~kwd2 }% __ONLY ONE__ keyword per line