version 1.3

.Rd2dvi/Rd2.tex

@@ -0,0 +1,14 @@
+\nonstopmode{}
+\documentclass[a4paper]{book}
+\usepackage[times,hyper]{Rd}
+\usepackage{makeidx}
+\makeindex{}
+\begin{document}
+\chapter*{}
+\begin{center}
+{\textbf{\huge \R{} documentation}} \par\bigskip{{\Large of \file{catmap}}}
+\par\bigskip{\large \today}
+\end{center}
+
+\printindex{}
+\end{document}

.Rd2dvi/Rd2.tex.pre

@@ -0,0 +1,15 @@
+\nonstopmode{}
+\documentclass[a4paper]{book}
+\usepackage[times,hyper]{Rd}
+\usepackage{makeidx}
+\usepackage[@ENC@]{inputenc}
+\makeindex{}
+\begin{document}
+\chapter*{}
+\begin{center}
+{\textbf{\huge \R{} documentation}} \par\bigskip{{\Large of \file{catmap}}}
+\par\bigskip{\large \today}
+\end{center}
+
+\printindex{}
+\end{document}

DESCRIPTION

@@ -1,9 +1,9 @@
 Package: catmap
-Version: 1.2
-Date: 2007-06-09
+Version: 1.3
+Date: 2007-11-19
 Title: Case-control And Tdt Meta-Analysis Package
-Author: Kristin K. Nicodemus <knicodem@jhsph.edu> 
-Maintainer: Kristin K. Nicodemus <knicodem@jhsph.edu> 
-Description: catmap is an R package that conducts fixed-effects (inverse variance) and random-effects (DerSimonian and Laird, 1986) meta-analyses of case-control or family-based (TDT) genetic data; in addition, it performs meta-analyses combining these two types of study designs.  The fixed-effects model was first described by Kazeem and Farrell (2005); the random-effects model is described in Nicodemus (submitted).}
+Author: Kristin K. Nicodemus <kristin.nicodemus@well.ox.ac.uk> 
+Maintainer: Kristin K. Nicodemus <kristin.nicodemus@well.ox.ac.uk> 
+Description: catmap is an R package that conducts fixed-effects (inverse variance) and random-effects (DerSimonian and Laird, 1986) meta-analyses of case-control or family-based (TDT) genetic data; in addition, it performs meta-analyses combining these two types of study designs.  The fixed-effects model was first described by Kazeem and Farrell (2005); the random-effects model is described in Nicodemus (submitted).
 License: GPL (version 2 or newer) 
-Packaged: Wed Jun 20 13:12:11 2007; Owner
+Packaged: Mon Nov 19 12:20:01 2007; knicodemus

R/catmap.R

@@ -2,6 +2,14 @@ catmap<-function(dataset, ci, printout){
 options(warn=-1)
 data(catmapdata)
 
+#make defaults for catmap of 0.95 for CI and printout = TRUE
+if(missing(ci)){
+ci<-0.95
+}
+if(missing(printout)){
+printout<-TRUE
+}
+
 #read in data from function
 if(dataset!=catmapdata){
 a1<-read.table(dataset, header=T)

data/catmapdata.txt

@@ -0,0 +1,7 @@
+name	study	t	nt	caserisk	controlrisk	casenotrisk	controlnotrisk
+Peter,2002	2	0	0	316	338	220	218
+Abrams,2001	2	0	0	710	146	422	96
+Todd,2003	2	0	0	1004	344	233	543
+Yu,2007	2	0	0	3344	434	544	322
+Wei,2007	1	65	32	0	0	0	0
+

man/catmap.Rd

@@ -2,18 +2,18 @@
 \alias{catmap}
 \docType{package}
 \title{catmap: Case-control And TDT Meta-Analysis Package} 
-\author{Kristin K. Nicodemus, \email{nicodemusk@mail.nih.gov} or \email{knicodem@jhsph.edu}}
+\author{Kristin K. Nicodemus, \email{kristin.nicodemus@well.ox.ac.uk}}
 \description{ 
-\code{catmap} is an R package that conducts fixed-effects (inverse variance) and random-effects (DerSimonian and Laird, 1986) meta-analyses of case-control or family-based (TDT) genetic data; in addition, it performs meta-analyses combining these two types of study designs.  The fixed-effects model was first described by Kazeem and Farrell (2005); the random-effects model is described in Nicodemus (submitted).
+\code{catmap} is an R package that conducts fixed-effects (inverse variance) and random-effects (DerSimonian and Laird, 1986) meta-analyses of case-control or family-based (TDT) genetic data; in addition, it performs meta-analyses combining these two types of study designs.  The fixed-effects model was first described by Kazeem and Farrall (2005); the random-effects model is described in Nicodemus (submitted) and saves a text file to the current working directory of all results printed to screen (use getwd() to find cwd).
 } 
 \usage{catmapobject<-catmap(dataset, ci, printout) } 
 \arguments{
-	\item{dataset}{A text file containing a header with the following column names: \bold{name, study, t, nt, caserisk, controlrisk, casenotrisk, controlnotrisk} in tab-delimited format.  Note that the header must be exactly as specified and that all cells in the table must have an entry, even if the entry is 0 or missing (NA).  See for example: data(catmapdata).
+	\item{dataset}{A text file containing a header with the following column names: \bold{name, study, t, nt, caserisk, controlrisk, casenotrisk, controlnotrisk} in tab-delimited format.  Note that the header must be exactly as specified and that all cells in the table must have an entry, even if the entry is 0 or missing (NA).  See for example: data(catmapdata). \bold{The dataset argument to catmap should be either the example data or a file containing the data for catmap, not an R object.}
 }   
-	\item{ci}{The confidence level for confidence intervals; 0 < ci < 1}   
-	\item{printout}{Logical.  Should a text file of the fixed- and random-effects models and Q statistic results be saved to the current working directory?  Output files are saved with the default name of \bold{dataset.output.txt} where dataset is the name of the file given as the first argument to catmap.}
+	\item{ci}{The confidence level for confidence intervals; 0 < ci < 1.  The default is 0.95}   
+	\item{printout}{Logical.  Should a text file of the fixed- and random-effects models and Q statistic results be saved to the current working directory?  Output files are saved with the default name of \bold{dataset.output.txt} where dataset is the name of the file given as the first argument to catmap.  Default = TRUE.}
 }
-\details{catmap is an R package that conducts fixed-effects (inverse variance) and random-effects (DerSimonian and Laird, 1986) meta-analyses of case-control or family-based (TDT) genetic data; in addition, it performs meta-analyses combining these two types of study designs.  The fixed-effects model was first described by Kazeem and Farrell (2005); the random-effects model is described in Nicodemus (submitted). Cumulative meta-analyses over time and leave-one-out sensitivity analyses may be performed using either fixed- or random-effects estimates or both estimates may be calculated; both produce a .txt file and an optional .pdf plot as output. A funnel plot graphic is implemented; however, no formal test of publication bias is available (see Ioannidis & Trikalinos, 2007).  \bold{Note that a catmap object must be created on the first call to catmap.} 
+\details{catmap is an R package that conducts fixed-effects (inverse variance) and random-effects (DerSimonian and Laird, 1986) meta-analyses of case-control or family-based (TDT) genetic data; in addition, it performs meta-analyses combining these two types of study designs.  The fixed-effects model was first described by Kazeem and Farrall (2005); the random-effects model is described in Nicodemus (submitted). Cumulative meta-analyses over time and leave-one-out sensitivity analyses may be performed using either fixed- or random-effects estimates or both estimates may be calculated; both produce a .txt file and an optional .pdf plot as output. A funnel plot graphic is implemented; however, no formal test of publication bias is available (see Ioannidis & Trikalinos, 2007). If users request a file to be created containing the results the file will be saved to the current working directory, which users can find by using >getwd(). \bold{Note that a catmap object must be created on the first call to catmap. If you do not create a catmap object you will not be able to use any of the other functions AND you will get a printout of the entire contents to screen} 
 } 
 \seealso{
   \code{\link{catmap.forest}},

man/catmap.cumulative.Rd

@@ -1,9 +1,9 @@
 \name{catmap.cumulative} 
 \alias{catmap.cumulative}
 \title{Cumulative Meta-Analyses and Plots using either Fixed- or Random-Effects} 
-\author{Kristin K. Nicodemus, \email{nicodemusk@mail.nih.gov} or \email{knicodem@jhsph.edu}}
+\author{Kristin K. Nicodemus, \email{kristin.nicodemus@well.ox.ac.uk}}
 \description{ 
-\code{catmap.cumulative} conducts cumulative meta-analyses and creates plots of the ORs and confidence intervals using either fixed- or random-effects analyses.
+\code{catmap.cumulative} conducts cumulative meta-analyses and creates plots of the ORs and confidence intervals using either fixed- or random-effects analyses, and saves text files and plot files to the current working directory (use getwd() to obtain the current working directory). The plots are not created in the R Graphics device.
 } 
 \usage{catmap.cumulative(catmapobject, fe.cumulative, re.cumulative, fe.cumplot, 
 re.cumplot) } 

man/catmap.forest.Rd

@@ -1,9 +1,9 @@
 \name{catmap.forest} 
 \alias{catmap.forest}
 \title{Forest Plots using either Fixed- or Random-Effects Pooled ORs and CIs} 
-\author{Kristin K. Nicodemus, \email{nicodemusk@mail.nih.gov} or \email{knicodem@jhsph.edu}}
+\author{Kristin K. Nicodemus, \email{kristin.nicodemus@well.ox.ac.uk}}
 \description{ 
-\code{catmap.forest} creates forest plots of the individual study ORs and CIs and the fixed or random effects pooled OR and CI.
+\code{catmap.forest} creates forest plots of the individual study ORs and CIs and the fixed or random effects pooled OR and CI and saves them to the current working directory (use getwd() to view cwd).  The plots are not created in the R Graphics device.
 } 
 \usage{catmap.forest(catmapobject, fe.forest, re.forest) } 
 \arguments{
@@ -12,7 +12,7 @@
 	\item{re.forest}{Logical.  Should a forest plot be created using the random-effects estimates?  Plots are saved with the default name of \bold{dataset.random.effects.forest.pdf} where dataset is the name of the file given as the first argument to catmap.}
 }
 \details{
-\code{catmap.forest} creates forest plots of individual study ORs and CIs plus the pooled estimate of the fixed- or random-effects pooled OR and CI.
+\code{catmap.forest} creates forest plots of individual study ORs and CIs plus the pooled estimate of the fixed- or random-effects pooled OR and CI. Plots are not created in the R Graphics device window, but are instead saved to a .pdf file in the current working directory, which can be found using getwd()
 } 
 \seealso{
   \code{\link{catmap}},

man/catmap.funnel.Rd

@@ -1,16 +1,16 @@
 \name{catmap.funnel} 
 \alias{catmap.funnel}
 \title{Funnel Plots for catmap} 
-\author{Kristin K. Nicodemus, \email{nicodemusk@mail.nih.gov} or \email{knicodem@jhsph.edu}}
+\author{Kristin K. Nicodemus, \email{kristin.nicodemus@well.ox.ac.uk}}
 \description{ 
-\code{catmap.funnel} creates a funnel plot of the individual ORs against the se.
+\code{catmap.funnel} creates a funnel plot of the individual ORs against the se and saves the file to the current working directory (use getwd() to view).  The plots are not created in the R Graphics device.
 } 
 \usage{catmap.funnel(catmapobject, funnel) } 
 \arguments{
 	\item{catmapobject}{The catmap object created by a previous call to catmap}   
 	\item{funnel}{Logical.  Should a funnel plot be produced?  Funnel plots plot standard error of the log ORs against the ORs along with a solid line at 1.0 and a dotted line at the overall pooled OR.  Used to assess publication bias.  Output plot file is saved with the default name of \bold{dataset.funnel.plot.pdf} where dataset is the name of the file given as the first argument to catmap.}
 } 
-\details{\code{catmap.funnel} creates a .pdf file of the funnel plot.
+\details{\code{catmap.funnel} creates a .pdf file of the funnel plot. Plots are not created in the R Graphics device window, but are instead saved to a .pdf file in the current working directory.
 } 
 \seealso{
   \code{\link{catmap}},

man/catmap.sense.Rd

@@ -1,9 +1,9 @@
 \name{catmap.sense} 
 \alias{catmap.sense}
 \title{Leave-One-Out Sensitivity Analyses and Plots using either Fixed- or Random-Effects Estimates} 
-\author{Kristin K. Nicodemus, \email{nicodemusk@mail.nih.gov} or \email{knicodem@jhsph.edu}}
+\author{Kristin K. Nicodemus, \email{kristin.nicodemus@well.ox.ac.uk}}
 \description{ 
-\code{catmap.sense} conducts leave-one-out sensitivity analyses and creates plots of the ORs and confidence intervals using either fixed- or random-effects analyses.
+\code{catmap.sense} conducts leave-one-out sensitivity analyses and creates plots of the ORs and confidence intervals using either fixed- or random-effects analyses, which are saved to the current working directory (use getwd() to view) but does not create the plots in the R Graphics device.
 } 
 \usage{catmap.sense(catmapobject, fe.sense, re.sense, fe.senseplot, re.senseplot) } 
 \arguments{
@@ -14,7 +14,7 @@
 	\item{re.senseplot}{Logical.  Should a .pdf plot of the ORs and CIs from the sensitivity analysis using random-effects be output?  Can be TRUE only if re.sense=TRUE.  Output plot file is saved with the default name of \bold{dataset.random.effects.sensitivity.plot. pdf} where dataset is the name of the file given as the first argument to catmap.}
 }
 \details{
-\code{catmap.sense} conducts leave-one-out sensitivity analyses and creates .pdf files of plots of the ORs and CIs using either the fixed-effect or the random-effect estimates. 
+\code{catmap.sense} conducts leave-one-out sensitivity analyses and creates .pdf files of plots of the ORs and CIs using either the fixed-effect or the random-effect estimates. Plots are not created in the R Graphics device window, but are instead saved to a .pdf file in the current working directory. Likewise the .txt files of results will be saved to the current working directory. To find the current working directory, use getwd()
 }
 \seealso{
   \code{\link{catmap}},

man/catmapdata.Rd

@@ -2,7 +2,7 @@
 \alias{catmapdata}
 \docType{data}
 \title{An example data frame for use with catmap}
-\author{Kristin K. Nicodemus, \email{nicodemusk@mail.nih.gov} or \email{knicodem@jhsph.edu}}
+\author{Kristin K. Nicodemus, \email{kristin.nicodemus@well.ox.ac.uk}}
 \description{
 A file for use with \code{catmap} containing simulated data.
 }