Update an existing meta-analysis object.
# S3 method for meta
update(
object,
data = object$data,
subset,
studlab,
exclude,
cluster,
method = object$method,
sm = object$sm,
incr,
method.incr = object$method.incr,
allstudies = object$allstudies,
MH.exact = object$MH.exact,
RR.Cochrane = object$RR.Cochrane,
Q.Cochrane = object$Q.Cochrane,
model.glmm = object$model.glmm,
level = object$level,
level.ma = object$level.ma,
common = object$common,
random = object$random,
overall = object$overall,
overall.hetstat = object$overall.hetstat,
method.random.ci = object$method.random.ci,
adhoc.hakn.ci = object$adhoc.hakn.ci,
method.predict = object$method.predict,
adhoc.hakn.pi = object$adhoc.hakn.pi,
method.tau = object$method.tau,
method.tau.ci = object$method.tau.ci,
tau.preset = object$tau.preset,
TE.tau = object$TE.tau,
tau.common = object$tau.common,
prediction = object$prediction | !missing(method.predict),
level.predict = object$level.predict,
null.effect = object$null.effect,
method.bias = object$method.bias,
backtransf = object$backtransf,
pscale = object$pscale,
irscale = object$irscale,
irunit = object$irunit,
text.common = object$text.common,
text.random = object$text.random,
text.predict = object$text.predict,
text.w.common = object$text.w.common,
text.w.random = object$text.w.random,
title = object$title,
complab = object$complab,
outclab = object$outclab,
label.e = object$label.e,
label.c = object$label.c,
label.left = object$label.left,
label.right = object$label.right,
n.e = object$n.e,
n.c = object$n.c,
pooledvar = object$pooledvar,
method.smd = object$method.smd,
sd.glass = object$sd.glass,
exact.smd = object$exact.smd,
method.ci = object$method.ci,
subgroup,
subgroup.name = object$subgroup.name,
print.subgroup.name = object$print.subgroup.name,
sep.subgroup = object$sep.subgroup,
test.subgroup = object$test.subgroup,
prediction.subgroup = object$prediction.subgroup,
byvar,
id,
print.CMH = object$print.CMH,
keepdata = TRUE,
left = object$left,
ma.common = object$ma.common,
type = object$type,
n.iter.max = object$n.iter.max,
warn = FALSE,
warn.deprecated = gs("warn.deprecated"),
verbose = FALSE,
control = object$control,
...
)An object of class "meta" and "metabin",
"metacont", "metacor", "metainc",
"metagen", "metamean", "metaprop", or
"metarate" (see meta-object).
An object of class meta.
Dataset.
Subset.
Study label.
An optional vector specifying studies to exclude from meta-analysis, however, to include in printouts and forest plots.
An optional vector specifying which estimates come from the same cluster resulting in the use of a three-level meta-analysis model.
A character string indicating which method is to be
used for pooling of studies; see metabin and
metainc function for admissible values.
A character string indicating which summary measure is used for pooling.
Either a numerical value or vector which can be added
to each cell frequency for studies with a zero cell count or the
character string "TA" which stands for treatment arm
continuity correction.
A character string indicating which continuity
correction method should be used ("only0",
"if0all", or "all").
A logical indicating if studies with zero or all
events in both groups are to be included in the meta-analysis
(applies only if sm is equal to "RR" or
"OR").
A logical indicating if incr is not to be
added to all cell frequencies for studies with a zero cell count
to calculate the pooled estimate based on the Mantel-Haenszel
method.
A logical indicating if 2*incr instead of
1*incr is to be added to n.e and n.c in the
calculation of the risk ratio (i.e., sm="RR") for studies
with a zero cell. This is used in RevMan 5, the program for
preparing and maintaining Cochrane reviews.
A logical indicating if the Mantel-Haenszel estimate is used in the calculation of the heterogeneity statistic Q which is implemented in RevMan 5, the program for preparing and maintaining Cochrane reviews.
A character string indicating which GLMM model should be used.
The level used to calculate confidence intervals for individual studies.
The level used to calculate confidence intervals for meta-analysis estimates.
A logical indicating whether a common effect meta-analysis should be conducted.
A logical indicating whether a random effects meta-analysis should be conducted.
A logical indicating whether overall summaries should be reported. This argument is useful in a meta-analysis with subgroups if overall results should not be reported.
A logical value indicating whether to print heterogeneity measures for overall treatment comparisons. This argument is useful in a meta-analysis with subgroups if heterogeneity statistics should only be printed on subgroup level.
A character string indicating which method
is used to calculate confidence interval and test statistic for
random effects estimate (see meta-package).
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).
A character string indicating which method is
used to calculate a prediction interval (see
meta-package).
A character string indicating whether an
ad hoc variance correction should be applied for
prediction interval (see meta-package).
A character string indicating which method is
used to estimate the between-study variance \(\tau^2\) and its
square root \(\tau\) (see meta-package).
A character string indicating which method is
used to estimate the confidence interval of \(\tau^2\) and
\(\tau\) (see meta-package).
Prespecified value for the square root of the between-study variance \(\tau^2\).
Overall treatment effect used to estimate the between-study variance tau-squared.
A logical indicating whether tau-squared should be the same across subgroups.
A logical indicating whether a prediction interval should be printed.
The level used to calculate prediction interval for a new study.
A numeric value specifying the effect under the null hypothesis.
A character string indicating which test for
funnel plot asymmetry is to be used, can be abbreviated. See
function metabias.
A logical indicating whether results should be
back transformed in printouts and plots. If backtransf =
TRUE, 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.
A numeric giving scaling factor for printing of
single event probabilities or risk differences, i.e. if argument
sm is equal to "PLOGIT", "PLN",
"PRAW", "PAS", "PFT", or "RD".
A numeric defining a scaling factor for printing of
single incidence rates or incidence rate differences, i.e. if
argument sm is equal to "IR", "IRLN",
"IRS", "IRFT", or "IRD".
A character specifying the time unit used to calculate rates, e.g. person-years.
A character string used in printouts and forest plot to label the pooled common effect estimate.
A character string used in printouts and forest plot to label the pooled random effects estimate.
A character string used in printouts and forest plot to label the prediction interval.
A character string used to label weights of common effect model.
A character string used to label weights of random effects model.
Title of meta-analysis / systematic review.
Comparison label.
Outcome label.
Label for experimental group.
Label for control group.
Graph label on left side of forest plot.
Graph label on right side of forest plot.
Number of observations in experimental group. (only for metagen object)
Number of observations in control group. (only for metagen object)
A logical indicating if a pooled variance should
be used for the mean difference (only for metacont object with
sm = "MD").
A character string indicating which method is
used to estimate the standardised mean difference (only for
metacont object with sm = "SMD"). Either "Hedges"
for Hedges' g (default), "Cohen" for Cohen's d, or
"Glass" for Glass' delta, can be abbreviated.
A character string indicating which standard
deviation is used in the denominator for Glass' method to
estimate the standardised mean difference (only for metacont
object with sm = "SMD"). Either "control" using the
standard deviation in the control group (sd.c) or
"experimental" using the standard deviation in the
experimental group (sd.e), can be abbreviated.
A logical indicating whether exact formulae should be used in estimation of the standardised mean difference and its standard error.
A character string indicating which method is used
to calculate confidence intervals for individual studies. Either
"z", "t", "WS", "WSCC", "AC",
"SA", "SACC", "NAsm", or "Poisson",
can be abbreviated. See functions metacont,
metaprop and metarate.
An optional vector to conduct a meta-analysis with subgroups.
A character string with a name for the subgroup variable.
A logical indicating whether the name of the subgroup variable should be printed in front of the group labels.
A character string defining the separator between name of subgroup variable and subgroup label.
A logical value indicating whether to print results of test for subgroup differences.
A logical indicating whether prediction intervals should be printed for subgroups.
Deprecated argument (replaced by 'subgroup').
Deprecated argument (replaced by 'cluster').
A logical indicating whether result of the Cochran-Mantel-Haenszel test for overall effect should be printed.
A logical indicating whether original data (set) should be kept in meta object.
A logical indicating whether studies are supposed to be
missing on the left or right side of the funnel plot. If NULL,
the linear regression test for funnel plot symmetry (i.e.,
function metabias(..., method = "linreg")) is used to
determine whether studies are missing on the left or right side.
A logical indicating whether a common effect or random effects model is used to estimate the number of missing studies.
A character indicating which method is used to estimate
the number of missing studies. Either "L" or "R".
Maximum number of iterations to estimate number of missing studies.
A logical indicating whether warnings should be printed
(e.g., if incr is added to studies with zero cell
frequencies).
A logical indicating whether warnings should be printed if deprecated arguments are used.
A logical indicating whether to print information on updates of older meta versions.
An optional list to control the iterative process to
estimate the between-study variance \(\tau^2\). This argument
is passed on to rma.uni or
rma.glmm, respectively.
Additional arguments (ignored at the moment).
Guido Schwarzer guido.schwarzer@uniklinik-freiburg.de
Wrapper function to update an existing meta-analysis object which
was created with R function metabin,
metacont, metacor,
metagen, metainc,
metamean, metaprop, or
metarate. More details on function arguments are
available in help files of respective R functions.
This function can also be used for objects of class 'trimfill', 'metacum', and 'metainf'.
metabin, metacont,
metacor, metagen,
metainc, metamean,
metaprop, metarate
data(Fleiss1993cont)
m1 <- metacont(n.psyc, mean.psyc, sd.psyc, n.cont, mean.cont, sd.cont,
data = Fleiss1993cont, studlab = paste(study, year), sm = "SMD")
m1
# Change summary measure (from 'SMD' to 'MD')
#
update(m1, sm = "MD")
# Restrict analysis to subset of studies
#
update(m1, subset = 1:2)
# Use different levels for confidence intervals
#
m2 <- update(m1, level = 0.66, level.ma = 0.99)
print(m2, digits = 2)
forest(m2)
Run the code above in your browser using DataLab