Wrapper function to perform meta-analysis for a single outcome of a Cochrane Intervention review.
metacr(
x,
comp.no = 1,
outcome.no = 1,
method,
sm,
level = gs("level"),
common,
random,
prediction = gs("prediction") | !missing(method.predict),
method.tau = "DL",
method.tau.ci = gs("method.tau.ci"),
level.hetstat = gs("level.hetstat"),
tau.common = FALSE,
method.I2 = gs("method.I2"),
level.ma = gs("level.ma"),
method.random.ci = "classic",
adhoc.hakn.ci = gs("adhoc.hakn.ci"),
level.predict = gs("level.predict"),
method.predict = gs("method.predict"),
adhoc.hakn.pi = gs("adhoc.hakn.pi"),
seed.predict = NULL,
Q.Cochrane,
swap.events,
logscale,
backtransf = gs("backtransf"),
test.subgroup,
prediction.subgroup = gs("prediction.subgroup"),
seed.predict.subgroup = NULL,
rob = NULL,
tool = NULL,
categories = NULL,
col = NULL,
symbols = NULL,
text.common = gs("text.common"),
text.random = gs("text.random"),
text.predict = gs("text.predict"),
text.w.common = gs("text.w.common"),
text.w.random = gs("text.w.random"),
title,
complab,
outclab,
label.left,
label.right,
col.label.left = gs("col.label.left"),
col.label.right = gs("col.label.right"),
keepdata = gs("keepdata"),
warn = FALSE,
warn.deprecated = gs("warn.deprecated"),
...
)An object of class "meta" and - depending on outcome type
utilised in Cochrane intervention review for selected outcome -
"metabin", "metacont", or "metagen" with
corresponding generic functions (see meta-object).
An object of class rm5 or cdir created by R
function read.rm5 or read.cdir .
Comparison number.
Outcome number.
A character string indicating which method is to be
used for pooling of studies. One of "Inverse",
"MH", or "Peto", can be abbreviated.
A character string indicating which summary measure
("RR", "OR", "RD", "ASD",
"HR", "MD", or "SMD", or "ROM") is to
be used for pooling of studies.
The level used to calculate confidence intervals for individual studies.
A logical indicating whether a common effect meta-analysis should be conducted.
A logical indicating whether a random effects meta-analysis should be conducted.
A logical indicating whether a prediction interval should be printed.
A character string indicating which method is
used to estimate the between-study variance \(\tau^2\) and its
square root \(\tau\) (see meta-package).
A character string indicating which method is
used to estimate the confidence interval of \(\tau^2\) and
\(\tau\) (see meta-package).
The level used to calculate confidence intervals for heterogeneity statistics.
A logical indicating whether tau-squared should be the same across subgroups.
A character string indicating which method is
used to estimate the heterogeneity statistic I\(^2\). Either
"Q" or "tau2", can be abbreviated
(see meta-package).
The level used to calculate confidence intervals for meta-analysis estimates.
A character string indicating which method
is used to calculate confidence interval and test statistic for
random effects estimate (see meta-package).
A character string indicating whether an
ad hoc variance correction should be applied in the case
of an arbitrarily small Hartung-Knapp variance estimate (see
meta-package).
The level used to calculate prediction interval for a new study.
A character string indicating which method is
used to calculate a prediction interval (see
meta-package).
A character string indicating whether an
ad hoc variance correction should be applied for
prediction interval (see meta-package).
A numeric value used as seed to calculate
bootstrap prediction interval (see meta-package).
A logical indicating if the Mantel-Haenszel estimate is used in the calculation of the heterogeneity statistic Q which is implemented in RevMan 5.
A logical indicating whether events and non-events should be interchanged.
A logical indicating whether effect estimates are
entered on log-scale (ignored for cdir objects).
A logical indicating whether results should be
back transformed in printouts and plots. If
backtransf=TRUE (default), results for sm="OR" are
printed as odds ratios rather than log odds ratios and results
for sm="ZCOR" are printed as correlations rather than
Fisher's z transformed correlations, for example.
A logical value indicating whether to print results of test for subgroup differences.
A logical indicating whether prediction intervals should be printed for subgroups.
A numeric vector providing seeds to calculate bootstrap prediction intervals within subgroups. Must be of same length as the number of subgroups.
A logical indicating whether risk of bias (RoB)
assessment should be considered in meta-analysis (only for
read.cdir objects).
Risk of bias (RoB) tool (only for read.cdir
objects).
Possible RoB categories (only for
read.cdir objects).
Colours for RoB categories (only for read.cdir
objects).
Corresponding symbols for RoB categories (only for
read.cdir objects).
A character string used in printouts and forest plot to label the pooled common effect estimate.
A character string used in printouts and forest plot to label the pooled random effects estimate.
A character string used in printouts and forest plot to label the prediction interval.
A character string used to label weights of common effect model.
A character string used to label weights of random effects model.
Title of meta-analysis / systematic review.
Comparison label.
Outcome label.
Graph label on left side of null effect in forest plot.
Graph label on right side of null effect in forest plot.
The colour of the graph label on the left side of the null effect.
The colour of the graph label on the right side of the null effect.
A logical indicating whether original data (set) should be kept in meta object.
A logical indicating whether warnings should be printed
(e.g., if incr is added to studies with zero cell
frequencies).
A logical indicating whether warnings should be printed if deprecated arguments are used.
Additional arguments (to catch deprecated arguments).
Guido Schwarzer guido.schwarzer@uniklinik-freiburg.de
Cochrane intervention reviews are based on the comparison of two interventions. Each Cochrane intervention review can have a variable number of comparisons. For each comparison, a variable number of outcomes can be define. For each outcome, a separate meta-analysis is conducted. Review Manager 5 (RevMan 5) was the software used for preparing and maintaining Cochrane Reviews.
This wrapper function can be used to perform meta-analysis for a
single outcome of a Cochrane intervention review. Internally, R
functions metabin, metacont, and
metagen are called - depending on the definition of
the outcome in RevMan 5.
Information on the risk of bias RoB) assessment can be provided
with arguments tool, categories, col and
symbols. This is not useful if an overall RoB assessment has
been done. In this case use rob to add the full
flexible RoB information to a metacr object.
Note, it is recommended to choose the RevMan 5 settings before
executing metacr, i.e., settings.meta("revman5").
Review Manager (RevMan) [Computer program]. Version 5.4. The Cochrane Collaboration, 2020
meta-package, rob,
metabin, metacont,
metagen, read.cdir,
read.rm5, settings.meta
# 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)
# Choose RevMan 5 settings and store old settings
#
oldset <- settings.meta("revman5", quietly = FALSE)
# Same result as R command example(Fleiss1993bin)
#
metacr(Fleiss1993_CR)
# Same result as R command example(Fleiss1993cont)
#
metacr(Fleiss1993_CR, 1, 2)
forest(metacr(Fleiss1993_CR, 1, 2))
# Change summary measure to RR
#
m1 <- metacr(Fleiss1993_CR)
update(m1, sm="RR")
# Use old settings
#
settings.meta(oldset)
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