Update a meta-analysis object

Description

Update an existing meta-analysis object.

Usage

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## S3 method for class 'meta'
update(object, 
       data=object$data, subset=object$subset,
       studlab=object$data$.studlab,
       method=object$method, sm=object$sm,
       incr=object$incr, allincr=object$allincr,
       addincr=object$addincr, allstudies=object$allstudies,
       MH.exact=object$MH.exact, RR.cochrane=object$RR.cochrane,
       model.glmm = object$model.glmm,
       level=object$level, level.comb=object$level.comb,
       comb.fixed=object$comb.fixed, comb.random=object$comb.random,
       hakn=object$hakn, method.tau=object$method.tau,
       tau.preset=object$tau.preset,
       TE.tau=object$TE.tau, tau.common=object$tau.common,
       prediction=object$prediction, level.predict=object$level.predict,
       method.bias=object$method.bias, backtransf = object$backtransf,
       pscale = object$pscale, irscale = object$irscale, irunit = object$irunit,
       title=object$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$method.ci,
       byvar=object$byvar, bylab=object$bylab, print.byvar=object$print.byvar,
       byseparator = object$byseparator,
       print.CMH=object$print.CMH, keepdata=TRUE,
       left=object$left, ma.fixed=object$ma.fixed,
       type=object$type, n.iter.max=object$n.iter.max,
       warn=object$warn, ...)

Arguments

object

An object of class meta.

data

Dataset.

subset

Subset.

studlab

Study label.

method

A character string indicating which method is to be used for pooling of studies; see metabin and metainc function for admissible values.

sm

A character string indicating which summary measure is used for pooling.

incr

Could be either a numerical value which is added to each cell frequency for studies with a zero cell count or the character string "TA" which stands for treatment arm continuity correction.

allincr

A logical indicating if incr is added to each cell frequency of all studies if at least one study has a zero cell count. If FALSE (default), incr is added only to each cell frequency of studies with a zero cell count.

addincr

A logical indicating if incr is added to each cell frequency of all studies irrespective of zero cell counts.

allstudies

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").

MH.exact

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.

RR.cochrane

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 Cochrane Collaboration's program for preparing and maintaining Cochrane reviews.

model.glmm

A character string indicating which GLMM model should be used.

level

The level used to calculate confidence intervals for individual studies.

level.comb

The level used to calculate confidence intervals for pooled estimates.

comb.fixed

A logical indicating whether a fixed effect meta-analysis should be conducted.

comb.random

A logical indicating whether a random effects meta-analysis should be conducted.

hakn

A logical indicating whether the method by Hartung and Knapp should be used to adjust test statistics and confidence intervals.

method.tau

A character string indicating which method is used to estimate the between-study variance τ^2. Either "DL", "PM", "REML", "ML", "HS", "SJ", "HE", or "EB", can be abbreviated. See function metagen.

tau.preset

Prespecified value for the square-root of the between-study variance τ^2.

TE.tau

Overall treatment effect used to estimate the between-study variance τ^2.

tau.common

A logical indicating whether tau-squared should be the same across subgroups.

prediction

A logical indicating whether a prediction interval should be printed.

level.predict

The level used to calculate prediction interval for a new study.

method.bias

A character string indicating which test for funnel plot asymmetry is to be used. Either "rank", "linreg", "mm", "count", "score", or "peters", can be abbreviated. See function metabias

backtransf

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.

pscale

A numeric giving scaling factor for printing of single event probabilities, i.e. if argument sm is equal to "PLOGIT", "PLN", "PRAW", "PAS", or "PFT".

irscale

A numeric defining a scaling factor for printing of rates, i.e. if argument sm is equal to "IR", "IRLN", "IRS", or "IRFT".

irunit

A character specifying the time unit used to calculate rates, e.g. person-years.

title

Title of meta-analysis / systematic review.

complab

Comparison label.

outclab

Outcome label.

label.e

Label for experimental group.

label.c

Label for control group.

label.left

Graph label on left side of forest plot.

label.right

Graph label on right side of forest plot.

n.e

Number of observations in experimental group. (only for metagen object)

n.c

Number of observations in control group. (only for metagen object)

pooledvar

A logical indicating if a pooled variance should be used for the mean difference (only for metacont object with sm="MD").

method.smd

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.

sd.glass

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.

exact.smd

A logical indicating whether exact formulae should be used in estimation of the standardised mean difference and its standard error.

method.ci

A character string indicating which method is used to calculate confidence intervals for individual studies. Either "CP", "WS", "WSCC", "AC", "SA",, "SACC", or "NAsm", can be abbreviated. See function metaprop.

byvar

An optional vector containing grouping information (must be of same length as event.e).

bylab

A character string with a label for the grouping variable.

print.byvar

A logical indicating whether the name of the grouping variable should be printed in front of the group labels.

byseparator

A character string defining the separator between label and levels of grouping variable.

print.CMH

A logical indicating whether result of the Cochran-Mantel-Haenszel test for overall effect should be printed.

keepdata

A logical indicating whether original data (set) should be kept in meta object.

left

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.

ma.fixed

A logical indicating whether a fixed effect or random effects model is used to estimate the number of missing studies.

type

A character indicating which method is used to estimate the number of missing studies. Either "L" or "R".

n.iter.max

Maximum number of iterations to estimate number of missing studies.

warn

A logical indicating whether warnings should be printed (e.g., if incr is added to studies with zero cell frequencies).

...

Additional arguments (ignored at the moment).

Details

Wrapper function to update an existing meta-analysis object which was created with R function metabin, metacont, metagen, metacor, metainc, or metaprop.

This function can also be used for objects of class 'trimfill', 'metacum', and 'metainf'.

More details on function arguments are available in help files of respective R functions, i.e. metabin, metacont, ...

Value

An object of class "meta" and "metabin", "metacont", "metagen", "metaprop", or "metacor".

Author(s)

Guido Schwarzer sc@imbi.uni-freiburg.de

See Also

metabin, metacont, metagen, metaprop, metacor

Examples

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data(Fleiss93cont)
meta1 <- metacont(n.e, mean.e, sd.e, n.c, mean.c, sd.c,
                  data=Fleiss93cont, sm="SMD", studlab=study)
meta1

# Change summary measure (from 'SMD' to 'MD')
#
update(meta1, sm="MD")

# Restrict analysis to subset of studies
#
update(meta1, subset=1:2)

# Use different levels for confidence intervals
#
meta2 <- update(meta1, level=0.66, level.comb=0.99)
print(meta2, digits=2)
forest(meta2)

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