meta: settings.meta – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

settings.meta

Print and change default settings to conduct and print or plot meta-analyses in R package meta.

Description

Print and change default settings to conduct and print or plot meta-analyses in R package meta. The following general settings are available: Review Manager 5, Journal of the American Medical Association.

Usage

settings.meta(...)

Arguments

...

Arguments to change default settings.

Details

This function can be used to define defaults for several arguments (i.e., assignments using gs) of the following R functions: metabin, metacont, metacor, metacr, metagen, metainc, metaprop, metarate

Furthermore, some of these settings are considered to print meta-analysis results using print.meta and print.summary.meta, and to produce forest plots using forest.meta.

The function can be used to either change individual settings (see Examples) or use one of the following general settings:

settings.meta("revman5")
settings.meta("jama")
settings.meta("iqwig5")
settings.meta("iqwig6")
settings.meta("geneexpr")

The first command can be used to reproduce meta-analyses from Cochrane reviews conducted with Review Manager 5 (RevMan 5, https://training.cochrane.org/online-learning/core-software-cochrane-reviews/revman) and specifies to use a RevMan 5 layout in forest plots. The second command can be used to generate forest plots following instructions for authors of the Journal of the American Medical Association (https://jamanetwork.com/journals/jama/pages/instructions-for-authors/). The next commands implement the recommendations of the Institute for Quality and Efficiency in Health Care, Germany (IQWiG) accordinging to General Methods 5 and 6, respectively (https://www.iqwig.de/en/about-us/methods/methods-paper/). The last setting can be used to print p-values in scientific notation and to suppress the calculation of confidence intervals for the between-study variance.

RevMan 5 settings, in detail:

Argument	Value	Comment
`hakn`	FALSE	method not available in RevMan 5
`method.tau`	"DL"	only available method in RevMan 5
`tau.common`	FALSE	common between-study variance in subgroups
`MH.exact`	FALSE	exact Mantel-Haenszel method
`RR.Cochrane`	TRUE	calculation of risk ratios
`Q.Cochrane`	TRUE	calculation of heterogeneity statistic
`layout`	"RevMan5"	layout for forest plots
`test.overall`	TRUE	print information on test of overall effect
`digits.I2`	0	number of digits for I-squared measure
`digits.tau2`	2	number of digits for tau-squared
`digits.tau`	4	number of digits for square root of tau-squared
`CIbracket`,	"["
`CIseparator`	", "	print confidence intervals as "`[., .]`"

JAMA settings:

Argument	Value	Comment
`layout`	"JAMA"	layout for forest plots
`test.overall`	TRUE	print information on test of overall effect
`digits.I2`	0	number of digits for I-squared measure
`CIbracket`,	"("
`CIseparator`	"-"	print confidence intervals as "`(.-.)`"
`zero.pval`,	TRUE	print p-values with leading zero
`JAMA.pval`,	TRUE	round p-values to three digits (for 0.001 < p ≤ 0.01) or two digits (p > 0.01)

IQWiG, General Methods 5 settings:

Argument	Value	Comment
`hakn`	TRUE	Hartung-Knapp method
`prediction`	TRUE	Prediction interval

IQWiG, General Methods 6 settings:

Argument	Value	Comment
`hakn`	TRUE	Hartung-Knapp method
`adhoc.hakn`	"ci"	ad hoc variance correction
`method.tau`	"PM"	Paule-Mandel estimator for between-study variance
`prediction`	TRUE	Prediction interval

Settings for gene expression data:

Argument	Value	Comment
`scientific.pval`	TRUE	Scientific notation for p-values
`method.tau.ci`	FALSE	no confidence interval for
	between-study heterogeneity variance

A list of all arguments with current settings is printed using the command settings.meta("print").

In order to reset all settings of R package meta the command settings.meta("reset") can be used.

Author(s)

Guido Schwarzer sc@imbi.uni-freiburg.de

Examples

# Get listing of current settings
#
settings.meta("print")

# Meta-analyses using default settings
#
metabin(10, 20, 15, 20)
metaprop(4, 20)
metabin(10, 20, 15, 20, sm = "RD")
metaprop(4, 20, sm = "PLN")

# Change summary measure for R functions metabin and metaprop
# and store old settings
#
oldset <- settings.meta(smbin = "RD", smprop = "PLN")
#
metabin(10, 20, 15, 20)
metaprop(4, 20)

# Use old settings
#
settings.meta(oldset)

# Change level used to calculate confidence intervals
# (99%-CI for studies, 99.9%-CI for pooled effects)
#
metagen(1:3, 2:4 / 10, sm = "MD")
settings.meta(level = 0.99, level.comb = 0.999)
metagen(1:3, 2:4 / 10, sm = "MD")

# Always print a prediction interval
#
settings.meta(prediction = TRUE)
metagen(1:3, 2:4 / 10, sm = "MD")
metagen(4:6, 4:2 / 10, sm = "MD")

# Try to set unknown argument results in a warning
#
try(settings.meta(unknownarg = TRUE))

# Reset to default settings of R package meta
#
settings.meta("reset")
metabin(10, 20, 15, 20)
metaprop(4, 20)
metagen(1:3, 2:4 / 10, sm = "MD")

# Do not back transform results (e.g. print log odds ratios instead
# of odds ratios, print transformed correlations / proportions
# instead of correlations / proportions)
#
settings.meta(backtransf = FALSE)
metabin(10, 20, 15, 20)
metaprop(4, 20)
metacor(c(0.85, 0.7, 0.95), c(20, 40, 10))

# Forest plot using RevMan 5 style
#
settings.meta("revman5")
forest(metagen(1:3, 2:4 / 10, sm = "MD", comb.fixed = FALSE),
       label.left = "Favours A", label.right = "Favours B",
       colgap.studlab = "2cm",
       colgap.forest.left = "0.2cm")

# Forest plot using JAMA style
#
settings.meta("jama")
forest(metagen(1:3, 2:4 / 10, sm = "MD", comb.fixed = FALSE),
       label.left = "Favours A", label.right = "Favours B",
       colgap.studlab = "2cm",
       colgap.forest.left = "0.2cm")

# Use slightly different layout for confidence intervals
# (especially useful if upper confidence limit can be negative)
#
settings.meta(CIseparator = " - ")
forest(metagen(-(1:3), 2:4 / 10, sm="MD", comb.fixed=FALSE),
       label.left="Favours A", label.right="Favours B",
       colgap.studlab = "2cm",
       colgap.forest.left = "0.2cm")

# Use old settings
#
settings.meta(oldset)