View source: R/settings.meta.R
settings.meta | R Documentation |
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.
settings.meta(..., quietly = TRUE)
... |
Arguments to change default settings. |
quietly |
A logical indicating whether information on settings should be printed. |
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 and to produce forest plots.
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")
settings.meta("meta4")
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/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/).Study
labels according to JAMA guidelines can be generated using
labels.meta
.
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 setting "geneexpr"
can be used to print p-values in
scientific notation and to suppress the calculation of confidence
intervals for the between-study variance.
The last setting uses the default settings of R package meta, version 4 or below.
RevMan 5 settings, in detail:
Argument | Value | Comment |
method.random.ci | "classic" | only available method 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 |
prediction | FALSE | no prediction interval |
test.overall | TRUE | print information on test of overall effect |
test.subgroup | TRUE | print information on test for subgroup differences |
test.effect.subgroup | TRUE | print information on test for effect in subgroups |
digits.I2 | 0 | number of digits for I-squared measure |
digits.tau2 | 3 | number of digits for tau-squared |
digits.tau | 4 | number of digits for square root of tau-squared |
CIbracket , | "[" | |
CIseparator | ", " | print confidence intervals as
"[., .] " |
header.line , | TRUE | print header line |
JAMA settings:
Argument | Value | Comment |
layout | "JAMA" | layout for forest plots |
test.overall | TRUE | print information on test of overall effect |
test.subgroup | FALSE | print information on test for subgroup differences |
test.effect.subgroup | FALSE | print information on test for effect in subgroups |
digits.I2 | 0 | number of digits for I-squared measure |
digits.pval | 3 | number of digits for p-values |
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 \le 0.01) or two digits (p > 0.01) |
header.line , | TRUE | print header line |
IQWiG, General Methods 5 settings:
Argument | Value | Comment |
method.random.ci | "HK" | Hartung-Knapp method |
prediction | TRUE | Prediction interval |
IQWiG, General Methods 6 settings:
Argument | Value | Comment |
method.random.ci | "HK" | Hartung-Knapp method |
adhoc.hakn.ci | "IQWiG6" | 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 | ||
Settings for meta, version 4 or below:
Argument | Value | Comment |
method.tau | "DL" | DerSimonian-Laird estimator |
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")
or settings.meta(reset = TRUE)
can be used.
Guido Schwarzer guido.schwarzer@uniklinik-freiburg.de
gs
, forest.meta
,
print.meta
, labels.meta
# Get listing of current settings
#
settings.meta()
# 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.ma = 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", common = 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", common = 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", common = FALSE),
label.left = "Favours A", label.right = "Favours B",
colgap.studlab = "2cm", colgap.forest.left = "0.2cm")
# Use old settings
#
settings.meta(oldset)
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