[Rcolony-commits] r53 - pkg/man

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

Author: jonesor
Date: 2009-05-14 15:29:11 +0200 (Thu, 14 May 2009)
New Revision: 53

Added:
   pkg/man/testdata.Rd
Modified:
   pkg/man/get.interm.data.Rd
Log:
Added testdata.rd and replaced textit with emph in another file

Modified: pkg/man/get.interm.data.Rd
===================================================================
--- pkg/man/get.interm.data.Rd	2009-05-13 14:21:25 UTC (rev 52)
+++ pkg/man/get.interm.data.Rd	2009-05-14 13:29:11 UTC (rev 53)
@@ -17,30 +17,30 @@
 \details{
 The intermediate results available are:
 
-\textit{Run} : The replicate run number. Variable
-\textit{Tmr} : The number of temperature reductions so far within the run. Variable
-\textit{Itr} : The number of iterates (reconfigurations considered) so far within the run. Variable
-\textit{NSucc} : The number of successful (accepted) reconfigurations so far within the temperature. Variable
-\textit{NSuccLmt} : Maximum (Limit) number of successful reconfigurations allowed within the temperature. Constant
-\textit{NFail1} : The number of reconfigurations since the last update of the best likelihood within the temperature. Variable
-\textit{NFail1Lmt} : Maximum (Limit) value of  NFail1 within the temperature. Constant
-\textit{NFail2} : The total number of reconfigurations since the last update of the best likelihood within the run. Variable
-\textit{NFail2Lmt} : Maximum (Limit) value of  NFail2 within a run. Constant. The run terminates when NFail2Lmt=NFail2 and the successful rate (see below) < 0.01
-\textit{SucRate\%} : =NSucc / Itr. Variable
-\textit{SucLmt\%} : =NSucc / NSuccLmt. Variable
-\textit{FailLmt\%} : =NFail1 / NFail1Lmt. Variable
-\textit{IterLmt\%} : = (Number of iterates) / (Maximum number of iterates) within a temperature. Variable
-\textit{CrLogL} : The log likelihood of the current configuration. Variable
-\textit{#F1} : Current number of paternal sib families. Variable
-\textit{#F2} : Current number of maternal sib families. Variable
-\textit{#F3} : Current number of sib family clusters. Variable
-\textit{#FS} : Current number of full sib families. Variable
-\textit{HSPair} : Current number of half-sib dyads. Variable
-\textit{FSPair} : Current number of full-sib dyads. Variable
-\textit{#AssgnC1} : Current number of candidate males that are assigned parentage. Variable
-\textit{#AssgnC2} : Current number of candidate females that are assigned parentage. Variable
-\textit{#AssgnP1} : Current number of offspring that have assigned paternity. Variable
-\textit{#AssgnP2} : Current number of offspring that have assigned maternity. Variable
+\emph{Run} : The replicate run number. Variable
+\emph{Tmr} : The number of temperature reductions so far within the run. Variable
+\emph{Itr} : The number of iterates (reconfigurations considered) so far within the run. Variable
+\emph{NSucc} : The number of successful (accepted) reconfigurations so far within the temperature. Variable
+\emph{NSuccLmt} : Maximum (Limit) number of successful reconfigurations allowed within the temperature. Constant
+\emph{NFail1} : The number of reconfigurations since the last update of the best likelihood within the temperature. Variable
+\emph{NFail1Lmt} : Maximum (Limit) value of  NFail1 within the temperature. Constant
+\emph{NFail2} : The total number of reconfigurations since the last update of the best likelihood within the run. Variable
+\emph{NFail2Lmt} : Maximum (Limit) value of  NFail2 within a run. Constant. The run terminates when NFail2Lmt=NFail2 and the successful rate (see below) < 0.01
+\emph{SucRate\%} : =NSucc / Itr. Variable
+\emph{SucLmt\%} : =NSucc / NSuccLmt. Variable
+\emph{FailLmt\%} : =NFail1 / NFail1Lmt. Variable
+\emph{IterLmt\%} : = (Number of iterates) / (Maximum number of iterates) within a temperature. Variable
+\emph{CrLogL} : The log likelihood of the current configuration. Variable
+\emph{#F1} : Current number of paternal sib families. Variable
+\emph{#F2} : Current number of maternal sib families. Variable
+\emph{#F3} : Current number of sib family clusters. Variable
+\emph{#FS} : Current number of full sib families. Variable
+\emph{HSPair} : Current number of half-sib dyads. Variable
+\emph{FSPair} : Current number of full-sib dyads. Variable
+\emph{#AssgnC1} : Current number of candidate males that are assigned parentage. Variable
+\emph{#AssgnC2} : Current number of candidate females that are assigned parentage. Variable
+\emph{#AssgnP1} : Current number of offspring that have assigned paternity. Variable
+\emph{#AssgnP2} : Current number of offspring that have assigned maternity. Variable
 }
 \value{
   

Added: pkg/man/testdata.Rd
===================================================================
--- pkg/man/testdata.Rd	                        (rev 0)
+++ pkg/man/testdata.Rd	2009-05-14 13:29:11 UTC (rev 53)
@@ -0,0 +1,34 @@
+\name{testdata}
+\alias{testdata}
+
+\title{Example dataset for the rcolony package}
+\description{
+This is an example dataset, as would be obtained using \code{get.colony.data}}
+\usage{
+data(testdata)
+}
+\format{
+The datafile contains a list (\code{testdata}) as generated with  \code{get.colony.data}. There are nine variables: 
+\describe{
+\item{fathers}{Paternity data.}
+\item{mothers}{Maternity data.}
+\item{offspring}{Offspring data.}
+\item{maternity}{Maternity assignments.}
+\item{paternity}{Paternity assignments.}
+\item{pairwise.maternity}{Pairwise maternity assignments.}
+\item{pairwise.paternity}{Pairwise paternity assignments.}
+\item{sibs}{Sibship (half and full) assignments.}
+\item{pairwise.sibs}{Pairwise sibship (half and full) assignments.}
+
+
+}
+}
+
+
+\references{}
+\seealso{}
+
+% Add one or more standard keywords, see file 'KEYWORDS' in the
+% R documentation directory.
+\keyword{datasets}
+