metacr: Meta-analysis of outcome data from Cochrane review

In meta: General Package for Meta-Analysis

Meta-analysis of outcome data from Cochrane review

Description

Wrapper function to perform meta-analysis for a single outcome of a Cochrane Intervention review.

Usage

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,
  col.label.left = gs("col.label.left"),
  col.label.right = gs("col.label.right"),
  keepdata = gs("keepdata"),
  warn = FALSE,
  warn.deprecated = gs("warn.deprecated"),
  ...
)

Arguments

x	An object of class rm5 or cdir created by R function read.rm5 or read.cdir .
comp.no	Comparison number.
outcome.no	Outcome number.
method	A character string indicating which method is to be used for pooling of studies. One of "Inverse", "MH", or "Peto", can be abbreviated.
sm	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.
level	The level used to calculate confidence intervals for individual studies.
common	A logical indicating whether a common effect meta-analysis should be conducted.
random	A logical indicating whether a random effects meta-analysis should be conducted.
prediction	A logical indicating whether a prediction interval should be printed.
method.tau	A character string indicating which method is used to estimate the between-study variance \tau^2 and its square root \tau (see meta-package).
method.tau.ci	A character string indicating which method is used to estimate the confidence interval of \tau^2 and \tau (see meta-package).
level.hetstat	The level used to calculate confidence intervals for heterogeneity statistics.
tau.common	A logical indicating whether tau-squared should be the same across subgroups.
method.I2	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).
level.ma	The level used to calculate confidence intervals for meta-analysis estimates.
method.random.ci	A character string indicating which method is used to calculate confidence interval and test statistic for random effects estimate (see meta-package).
adhoc.hakn.ci	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).
level.predict	The level used to calculate prediction interval for a new study.
method.predict	A character string indicating which method is used to calculate a prediction interval (see meta-package).
adhoc.hakn.pi	A character string indicating whether an ad hoc variance correction should be applied for prediction interval (see meta-package).
seed.predict	A numeric value used as seed to calculate bootstrap prediction interval (see meta-package).
Q.Cochrane	A logical indicating if the Mantel-Haenszel estimate is used in the calculation of the heterogeneity statistic Q which is implemented in RevMan 5.
swap.events	A logical indicating whether events and non-events should be interchanged.
logscale	A logical indicating whether effect estimates are entered on log-scale (ignored for cdir objects).
backtransf	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.
test.subgroup	A logical value indicating whether to print results of test for subgroup differences.
prediction.subgroup	A logical indicating whether prediction intervals should be printed for subgroups.
seed.predict.subgroup	A numeric vector providing seeds to calculate bootstrap prediction intervals within subgroups. Must be of same length as the number of subgroups.
rob	A logical indicating whether risk of bias (RoB) assessment should be considered in meta-analysis (only for read.cdir objects).
tool	Risk of bias (RoB) tool (only for read.cdir objects).
categories	Possible RoB categories (only for read.cdir objects).
col	Colours for RoB categories (only for read.cdir objects).
symbols	Corresponding symbols for RoB categories (only for read.cdir objects).
text.common	A character string used in printouts and forest plot to label the pooled common effect estimate.
text.random	A character string used in printouts and forest plot to label the pooled random effects estimate.
text.predict	A character string used in printouts and forest plot to label the prediction interval.
text.w.common	A character string used to label weights of common effect model.
text.w.random	A character string used to label weights of random effects model.
title	Title of meta-analysis / systematic review.
complab	Comparison label.
outclab	Outcome label.
col.label.left	The colour of the graph label on the left side of the null effect.
col.label.right	The colour of the graph label on the right side of the null effect.
keepdata	A logical indicating whether original data (set) should be kept in meta object.
warn	A logical indicating whether warnings should be printed (e.g., if incr is added to studies with zero cell frequencies).
warn.deprecated	A logical indicating whether warnings should be printed if deprecated arguments are used.
...	Additional arguments (to catch deprecated arguments).

Details

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").

Value

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).

Author(s)

Guido Schwarzer [e-mail]

References

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

See Also

meta-package, rob, metabin, metacont, metagen, read.cdir, read.rm5, settings.meta

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)

# 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)

meta documentation built on Oct. 31, 2024, 5:07 p.m.