% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/read.rm5.R
\name{read.rm5}
\alias{read.rm5}
\alias{Fleiss1993_CR}
\title{Import RevMan 5 analysis data}
\usage{
read.rm5(
  file,
  sep = ",",
  quote = "\\"",
  title,
  numbers.in.labels = TRUE,
  debug = 0
)
}
\arguments{
\item{file}{The name of a file to read data values from.}

\item{sep}{The field separator character (only considered for
CSV-files). Values on each line of the file are separated by this
character. The comma is the default field separator character in
RevMan 5.}

\item{quote}{The set of quoting characters (only considered for
CSV-files). In RevMan 5 a "\"" is the default quoting character.}

\item{title}{Title of Cochrane review.}

\item{numbers.in.labels}{A logical indicating whether comparison
number and outcome number should be printed at the beginning of
the comparison (argument \code{complab}) and outcome label
(argument \code{outclab}); this is the default in RevMan 5.}

\item{debug}{An integer between 0 and 3 indicating whether to print
debug messages (only considered for RM5-files).}
}
\value{
A data frame containing the following components:
\item{comp.no}{Comparison number.}
\item{outcome.no}{Outcome number.}
\item{group.no}{Group number.}
\item{studlab}{Study label.}
\item{year}{Year of publication.}
\item{event.e}{Number of events in experimental group.}
\item{n.e}{Number of observations in experimental group.}
\item{event.c}{Number of events in control group.}
\item{n.c}{Number of observations in control group.}
\item{mean.e}{Estimated mean in experimental group.}
\item{sd.e}{Standard deviation in experimental group.}
\item{mean.c}{Estimated mean in control group.}
\item{sd.c}{Standard deviation in control group.}
\item{O.E}{Observed minus expected (IPD analysis).}
\item{V}{Variance of \code{O.E} (IPD analysis).}
\item{TE, seTE}{Estimated treatment effect and standard error of
  individual studies.}
\item{lower, upper}{Lower and upper limit of 95\% confidence
  interval for treatment effect in individual studies.}
\item{weight}{Weight of individual studies (according to
  meta-analytical method used in respective meta-analysis - see
  details).}
\item{order}{Ordering of studies.}
\item{grplab}{Group label.}
\item{type}{Type of outcome. D = dichotomous, C = continuous, P =
  IPD.}
\item{method}{A character string indicating which method has been
  used for pooling of studies. One of \code{"Inverse"},
  \code{"MH"}, or \code{"Peto"}.}
\item{sm}{A character string indicating which summary measure has
  been used for pooling of studies.}
\item{model}{A character string indicating which meta-analytical
  model has been used (either \code{"Fixed"} or \code{"Random"}).}
\item{common}{A logical indicating whether common effect
  meta-analysis has been used in respective meta-analysis (see
  details).}
\item{random}{A logical indicating whether random effects
  meta-analysis has been used in respective meta-analysis (see
  details).}
\item{outclab}{Outcome label.}
\item{k}{Total number of studies combined in respective
  meta-analysis).}
\item{event.e.pooled}{Number of events in experimental group in
  respective meta-analysis (see details).}
\item{n.e.pooled}{Number of observations in experimental group in
  respective meta-analysis (see details).}
\item{event.c.pooled}{Number of events in control group in
  respective meta-analysis (see details).}
\item{n.c.pooled}{Number of observations in control group in
  respective meta-analysis (see details).}
\item{TE.pooled}{Estimated treatment effect in respective
  meta-analysis (see details).}
\item{lower, upper}{Lower and upper limit of 95\% confidence
  interval for treatment effect in respective meta-analysis (see
  details).}
\item{weight.pooled}{Total weight in respective meta-analysis (see
  details).}
\item{Z.pooled}{Z-score for test of overall treatment effect in
  respective meta-analysis (see details).}
\item{pval.pooled}{P-value for test of overall treatment effect in
  respective meta-analysis (see details).}
\item{Q}{Heterogeneity statistic Q in respective meta-analysis (see
  details).}
\item{pval.Q}{P-value of heterogeneity statistic Q in respective
  meta-analysis (see details).}
\item{I2}{Heterogeneity statistic I\eqn{^2} in respective meta-analysis
  (see details).}
\item{tau2}{Between-study variance (moment estimator of
  DerSimonian-Laird) in respective meta-analysis.}
\item{Q.w}{Heterogeneity statistic Q within groups in respective
  meta-analysis (see details).}
\item{pval.Q.w}{P-value of heterogeneity statistic Q within groups
  in respective meta-analysis (see details).}
\item{I2.w}{Heterogeneity statistic I\eqn{^2} within groups in respective
  meta-analysis (see details).}
\item{label.e}{Label for experimental group.}
\item{label.c}{Label for control group.}
\item{label.left}{Graph label on left side of forest plot.}
\item{label.right}{Graph label on right side of forest plot.}
\item{complab}{Comparison label.}
}
\description{
Reads analysis data from Cochrane intervention review created with
RevMan 5 and creates a data frame from it.
}
\details{
Review Manager 5 (RevMan 5) was the software used for preparing and
maintaining Cochrane reviews
(\url{https://training.cochrane.org/online-learning/core-software/revman}).
RevMan 5 includes the ability to write systematic reviews of
interventions, diagnostic test accuracy reviews, methodology
reviews and overviews of reviews.

This function provides the ability to read the analysis data from a
Cochrane intervention review created with RevMan 5; a data frame is
created from it. Cochrane intervention reviews are based on
comparisons of two interventions.

By default in RevMan 5, the name of the exported CSV data file is
the title of the Cochrane review. Furthermore, the title is part of
the RM5-file. Argument \code{title} can be used to overwrite the
title of the Cochrane review.

\subsection{Import RM5-file}{

A RM5-file (which is in a specific XML format) can be used directly
to import the analysis dataset.

If the import fails, use argument \code{debug = 3} for more details.
}

\subsection{Import CSV-file}{

In the past, the following (rather complicated) procedure based on
a CSV-file generated within RevMan 5 was necessary - which is only
described here for backward compatibility.

In order to generate a data analysis file in RevMan 5 use the
following Menu points: \code{"File"} - \code{"Export"} -
\code{"Data and analyses"}. It is mandatory to include the
following fields in the exported data file by selecting them with
the mouse cursor in the Export Analysis Data Wizard: (i) Comparison
Number, (ii) Outcome Number, (iii) Subgroup Number. When these
fields are not selected a corresponding error message will be
printed in R.  It is recommended to include all fields in the
exported data file except for the last field
"Risk of bias tables". For example, in order to redo the
meta-analysis in R for the RevMan 5 data type
\code{"O-E and Variance"} the fields \code{"O-E"} and
\code{"Variance"} have to be selected in the Export Analysis Data
Wizard. If the last field "Risk of bias tables" is selected the
import in R fails with an error message
"line X did not have Y elements".
}
}
\examples{
# Locate export data file "Fleiss1993_CR.csv"
# in sub-directory of package "meta"
#
filename <- system.file("extdata", "Fleiss1993_CR.csv", package = "meta")
Fleiss1993_CR <- read.rm5(filename)

# Same result as R command example(Fleiss1993bin):
#
metacr(Fleiss1993_CR)

# Same result as R command example(Fleiss1993cont):
#
metacr(Fleiss1993_CR, 1, 2)

\dontrun{
# Locate file "Fleiss1993.rm5" in sub-directory of R package meta
#
filename <- system.file("extdata/Fleiss1993.rm5", package = "meta")
Fleiss1993_CR <- read.cdir(filename)
Fleiss1993_CR

# Same result as R Command example(Fleiss1993bin):
#
metacr(Fleiss1993_CR)
}

}
\references{
\emph{Review Manager (RevMan)} [Computer program]. Version 5.4.
The Cochrane Collaboration, 2020
}
\seealso{
\code{\link{summary.rm5}}, \code{\link{metabias.rm5}},
  \code{\link{metabin}}, \code{\link{metacont}},
  \code{\link{metagen}}, \code{\link{metacr}},
  \code{\link{print.rm5}}
}
\author{
Guido Schwarzer \email{guido.schwarzer@uniklinik-freiburg.de}
}
\keyword{datagen}
