
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(...)
Arguments to change default settings.
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")
The first command can be used to reproduce meta-analyses from Cochrane reviews conducted with Review Manager 5 (RevMan 5, http://community.cochrane.org/tools/review-production-tools/revman-5) 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 (http://jamanetwork.com/journals/jama/pages/instructions-for-authors).
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 |
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 |
0 | number of digits for tau-squared |
CIbracket , |
"[" |
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 , |
"(" |
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.
# NOT RUN {
#
# 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
#
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 = grid::unit(2, "cm"),
colgap.forest.left = grid::unit(0.2, "cm"))
#
# 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 = grid::unit(2, "cm"),
colgap.forest.left = grid::unit(0.2, "cm"))
#
# 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 = grid::unit(2, "cm"),
colgap.forest.left = grid::unit(0.2, "cm"))
# Use old settings
#
settings.meta(oldset)
# }
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