read.cdir: Import data of Cochrane intervention review

In guido-s/meta: General Package for Meta-Analysis

Import data of Cochrane intervention review

Description

Reads Cochrane data package (version 1) of a Cochrane intervention review and creates a data frame from it.

Usage

read.cdir(
  file,
  title = "Cochrane Review of Interventions",
  exdir = tempdir(),
  numbers.in.labels = TRUE,
  rob = !missing(tool) | !missing(categories) | !missing(col) | !missing(symbols),
  tool = NULL,
  categories = NULL,
  col = NULL,
  symbols = NULL,
  keep.orig = FALSE,
  ...
)

## S3 method for class 'cdir'
print(x, ...)

Arguments

file	The name of a file to read data values from.
title	Title of Cochrane review.
exdir	The directory to extract files to (the equivalent of ‘unzip -d’). It will be created if necessary.
numbers.in.labels	A logical indicating whether comparison number and outcome number should be printed at the beginning of the comparison (argument complab) and outcome label (argument outclab); this is the default in RevMan Web.
rob	A logical indicating whether risk of bias (RoB) assessment should be considered in meta-analyses.
tool	Risk of bias (RoB) tool.
categories	Possible RoB categories.
col	Colours for RoB categories.
symbols	Corresponding symbols for RoB categories.
keep.orig	A logical indicating whether to return the original data files.
...	Additional arguments (passed on to unzip)
x	An object of class "cdir".

Details

RevMan Web is the current software used for preparing and maintaining Cochrane reviews (https://training.cochrane.org/online-learning/core-software/revman). RevMan Web includes the ability to write systematic reviews of interventions or diagnostic test accuracy reviews.

This function provides the ability to read the Cochrane data package from a Cochrane intervention review created with RevMan Web. The ZIP-file is extracted with unzip.

Argument title can be used to overwrite the title of the Cochrane review.

Information on the risk of bias (RoB) assessment can be provided with arguments tool, categories, col and symbols. This is only useful if (i) all outcomes are based on the same RoB categories and (ii) an overall RoB assessment has not been done. If no overall RoB assessment was conducted, R function metacr can be used to provide the RoB information for a single outcome. R function rob is the most flexible way to add RoB information to a meta-analysis object.

Creation of Cochrane data package

Two possible ways exist to create the ZIP-file.

In RevMan Web (https://revman.cochrane.org/), press the "Export" button at the bottom of the Default view website. After a couple of seconds, the data package will be shown at the bottom of the Default view website under "Downloads".

In the Cochrane Library (https://www.cochranelibrary.com/), press on "Download statistical data" in the Contents menu to download an rm5-file. This file can be converted to a data package in RevMan Web using Help - Convert a RevMan 5 file.

Value

A list consisting of a data frame 'data' with the study data and (if available) a data frame 'rob' with information on the risk of bias assessment. If keep.orig = TRUE, an additional list 'orig' is returned containing elements 'settings', 'datarows', 'subgroup' and 'rob' (if available).

The data frame 'data' contains the following variables:

comp.no	Comparison number.
outcome.no	Outcome number.
group.no	Group number.
studlab	Study label.
year	Year of publication.
event.e	Number of events in experimental group.
n.e	Number of observations in experimental group.
event.c	Number of events in control group.
n.c	Number of observations in control group.
mean.e	Estimated mean in experimental group.
sd.e	Standard deviation in experimental group.
mean.c	Estimated mean in control group.
sd.c	Standard deviation in control group.
O.E	Observed minus expected (IPD analysis).
V	Variance of O.E (IPD analysis).
TE, seTE	Estimated treatment effect and standard error of individual studies.
lower, upper	Lower and upper limit of 95% confidence interval for treatment effect in individual studies.
weight	Weight of individual studies (according to meta-analytical method used in respective meta-analysis - see details).
order	Ordering of studies.
grplab	Group label.
type	Type of outcome. D = dichotomous, C = continuous, P = IPD.
method	A character string indicating which method has been used for pooling of studies. One of "Inverse", "MH", or "Peto".
sm	A character string indicating which summary measure has been used for pooling of studies.
model	A character string indicating which meta-analytical model has been used (either "Fixed" or "Random").
common	A logical indicating whether common effect meta-analysis has been used in respective meta-analysis (see details).
random	A logical indicating whether random effects meta-analysis has been used in respective meta-analysis (see details).
title	Title of Cochrane review.
complab	Comparison label.
outclab	Outcome label.
label.e	Label for experimental group.
label.c	Label for control group.
label.left	Graph label on left side of forest plot.
label.right	Graph label on right side of forest plot.

The data frame 'rob' contains the following variables:

studlab	Study label.
D1, D2, ...	Risk of bias domain 1, 2, ...
D1.details, D2.details, ...	Details on risk of bias domain 1, 2, ...

Author(s)

Guido Schwarzer [e-mail]

References

https://documentation.cochrane.org/revman-kb/data-package-user-guide-243761660.html

https://documentation.cochrane.org/revman-kb/data-package-specification-249561249.html

See Also

metacr, rob, read.rm5

Examples

# Locate file "Fleiss1993.zip" with Cochrane data package in
# sub-directory of R package meta
#
filename <- system.file("extdata/Fleiss1993.zip", package = "meta")
Fleiss1993_CR <- read.cdir(filename)
Fleiss1993_CR

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

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

guido-s/meta documentation built on April 18, 2024, 7:11 p.m.