settings.meta {meta} | R Documentation |
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(..., quietly = TRUE)
Arguments
... |
Arguments to change default settings. |
quietly |
A logical indicating whether information on settings should be printed. |
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 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("BMJ")
-
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 in BMJ layout.
The third 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 |
exact.smd | FALSE | exact formulae for Hedges' g and Cohen's d |
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 |
forest.I2 | TRUE | show heterogeneity statistic I2 in forest plots |
forest.tau2 | TRUE | show between-study heterogeneity variance in forest plots |
forest.tau | FALSE | do not show between-study heterogeneity standard deviation in forest plots |
forest.Q | TRUE | show heterogeneity statistic Q in forest plots |
forest.pval.Q | TRUE | show p-value of test for heterogeneity in forest plots |
forest.Rb | FALSE | do not show heterogeneity statistic Rb in forest plots |
digits.tau2 | 3 | number of digits for tau-squared |
digits.tau | 4 | number of digits for square root of tau-squared |
digits.I2 | 0 | number of digits for I-squared measure |
CIbracket , | "[" | |
CIseparator | ", " | print confidence intervals as
"[., .] " |
header.line , | TRUE | print header line |
BMJ settings:
Argument | Value | Comment |
layout | "BMJ" | 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 |
forest.I2 | TRUE | show heterogeneity statistic I2 in forest plots |
forest.tau2 | TRUE | show between-study heterogeneity variance in forest plots |
forest.tau | FALSE | do not show between-study heterogeneity standard deviation in forest plots |
forest.Q | TRUE | show heterogeneity statistic Q in forest plots |
forest.pval.Q | TRUE | show p-value of test for heterogeneity in forest plots |
forest.Rb | FALSE | do not show heterogeneity statistic Rb in forest plots |
digits.I2 | 0 | number of digits for I-squared measure |
digits.pval | 2 | number of digits for p-values |
CIbracket , | "(" | |
CIseparator | " to " | print confidence intervals as
"(. to .) " |
hetlab , | "Test for heterogeneity: " | |
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 |
forest.I2 | TRUE | show heterogeneity statistic I2 in forest plots |
forest.tau2 | FALSE | do not show between-study heterogeneity variance in forest plots |
forest.tau | FALSE | do not show between-study heterogeneity standard deviation in forest plots |
forest.Q | TRUE | show heterogeneity statistic Q in forest plots |
forest.pval.Q | TRUE | show p-value of test for heterogeneity in forest plots |
forest.Rb | FALSE | do not show heterogeneity statistic Rb in forest plots |
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 , | FALSE | 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.
Author(s)
Guido Schwarzer guido.schwarzer@uniklinik-freiburg.de
See Also
gs
, forest.meta
,
print.meta
, labels.meta
Examples
# 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)