[Rcolony-commits] r55 - pkg/man

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

Author: jonesor
Date: 2009-05-17 14:04:07 +0200 (Sun, 17 May 2009)
New Revision: 55

Modified:
   pkg/man/get.interm.data.Rd
   pkg/man/monitor.colony.Rd
Log:
Fixed get.interm.data (codoc mismatches)

Modified: pkg/man/get.interm.data.Rd
===================================================================
--- pkg/man/get.interm.data.Rd	2009-05-14 13:33:13 UTC (rev 54)
+++ pkg/man/get.interm.data.Rd	2009-05-17 12:04:07 UTC (rev 55)
@@ -3,15 +3,16 @@
 
 \title{ A function to collect intermediate data produced by Colony2 while it is running. }
 \description{
-While it is running, Colony2 produces output to indicate it's progress. This function allows R to import the outputs produced.}
-
+While it is running, Colony2 produces output to indicate the computation progress. This function allows R to import the outputs produced.}
+It is intended to be called from \code{\link{monitor.colony}} rather than being used directly by the user.
 \usage{
-get.interm.data(variable="CrLogL",datadir=getwd())
+get.interm.data(variable="CrLogL",datadir=getwd(),n=1)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
-  \item{variable}{The name of the variable required. }
-  \item{datadir}{ ~~Describe \code{colony.object} here~~ }
+  \item{variable}{The name of the variable that you wish to monitor. See details.}
+ \item{datadir}{The path to the directory that contains the Colony output files.}
+\item{n}{If there are two variables with the same name, which one should be used? See details.}
 
 }
 \details{
@@ -31,6 +32,8 @@
 \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{BtLogL} : The best log likelihood reached with 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
@@ -41,6 +44,11 @@
 \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
+
+F1, F2, F3, FS, HSPair, FSPair, AssgnC1, AssgnC2, AssgnP1 and AssgnP2 appear twice in the intermediate outputs of Colony2. Their first appearance is for the current status. While the second appearance is for the best status so far (i.e. the maximum value).
+Users wishing to plot any of these values should use the \emph{n} argument to select the appropriate value (1 for the current value, 2 for best value).
+
+
 }
 \value{
   

Modified: pkg/man/monitor.colony.Rd
===================================================================
--- pkg/man/monitor.colony.Rd	2009-05-14 13:33:13 UTC (rev 54)
+++ pkg/man/monitor.colony.Rd	2009-05-17 12:04:07 UTC (rev 55)
@@ -15,7 +15,7 @@
   \item{variable}{The name of the variable that you wish to monitor. See details.}
 \item{interv.t}{The interval (in seconds) at which R should retrieve intermediate data.}
   \item{last.few}{(not yet implemented) How many datapoints should be displayed. Set to -1 to show all data. If the number is a positive integer, then the last x datapoints are shown.}
-\item{n}{If there are two variables witht he same name, which one should be used? See details.}
+\item{n}{If there are two variables with the same name, which one should be used? See details.}
 \item{showres}{Should R show the results obtained in a table to be displayed in the R console window? Boolean.}