read.rm5: Import RevMan 5 analysis data

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/read.rm5.R

Description

Reads analysis data from Cochrane intervention review created with RevMan 5 and creates a data frame from it.

Usage

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read.rm5(
  file,
  sep = ",",
  quote = "\"",
  title,
  numbers.in.labels = TRUE,
  debug = 0
)

## S3 method for class 'rm5'
print(x, ...)

Arguments

file

The name of a file to read data values from.

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.

quote

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

title

Title of Cochrane review.

numbers.in.labels

A logical indicating whether comparision 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 5.

debug

An integer between 0 and 3 indicating whether to print debug messages (only considered for RM5-files).

x

An object of class rm5

...

Additional arguments (passed on to print.data.frame).

Details

Review Manager 5 (RevMan 5) was the software used for preparing and maintaining Cochrane reviews (https://training.cochrane.org/online-learning/core-software-cochrane-reviews/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 title can be used to overwrite the title of the Cochrane review.

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 debug = 3 for more details.

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: "File" - "Export" - "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 "O-E and Variance" the fields "O-E" and "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".

Value

A data frame containing the following components:

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 below for 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").

comb.fixed

A logical indicating whether fixed effect meta-analysis has been used in respective meta-analysis (see below for details).

comb.random

A logical indicating whether random effects meta-analysis has been used in respective meta-analysis (see below for details).

outclab

Outcome label.

k

Total number of studies combined in respective meta-analysis).

event.e.pooled

Number of events in experimental group in respective meta-analysis (see below for details).

n.e.pooled

Number of observations in experimental group in respective meta-analysis (see below for details).

event.c.pooled

Number of events in control group in respective meta-analysis (see below for details).

n.c.pooled

Number of observations in control group in respective meta-analysis (see below for details).

TE.pooled

Estimated treatment effect in respective meta-analysis (see below for details).

lower, upper

Lower and upper limit of 95% confidence interval for treatment effect in respective meta-analysis (see below for details).

weight.pooled

Total weight in respective meta-analysis (see below for details).

Z.pooled

Z-score for test of overall treatment effect in respective meta-analysis (see below for details).

pval.pooled

P-value for test of overall treatment effect in respective meta-analysis (see below for details).

Q

Heterogeneity statistic Q in respective meta-analysis (see below for details).

pval.Q

P-value of heterogeneity statistic Q in respective meta-analysis (see below for details).

I2

Heterogeneity statistic I^2 in respective meta-analysis (see below for details).

tau2

Between-study variance (moment estimator of DerSimonian-Laird) in respective meta-analysis.

Q.w

Heterogeneity statistic Q within groups in respective meta-analysis (see below for details).

pval.Q.w

P-value of heterogeneity statistic Q within groups in respective meta-analysis (see below for details).

I2.w

Heterogeneity statistic I^2 within groups in respective meta-analysis (see below for details).

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.

complab

Comparison label.

Author(s)

Guido Schwarzer sc@imbi.uni-freiburg.de

References

Review Manager (RevMan) [Computer program]. Version 5.4. The Cochrane Collaboration, 2020

See Also

summary.rm5, metabias.rm5, metabin, metacont, metagen, metacr

Examples

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# 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)

meta documentation built on Sept. 14, 2021, 5:14 p.m.