Print and summary method for objects of class meta

Description

Print and summary method for objects of class meta.

Usage

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
## S3 method for class 'meta'
print(x, sortvar,
        comb.fixed=x$comb.fixed,
        comb.random=x$comb.random,
        prediction=x$prediction,
        details=FALSE, ma=TRUE, backtransf=x$backtransf,
	pscale=x$pscale, irscale = x$irscale, irunit = x$irunit,
        digits = .settings$digits, digits.se = .settings$digits.se,
        digits.zval = .settings$digits.zval,
        digits.Q = .settings$digits.Q, digits.tau2 = .settings$digits.tau2,
        digits.H = .settings$digits.H, digits.I2 = .settings$digits.I2,
        digits.prop = .settings$digits.prop, digits.weight = .settings$digits.weight,
	warn.backtransf = FALSE,
        ...)

## S3 method for class 'metabias'
print(x, ...)

## S3 method for class 'meta'
summary(object,
        comb.fixed=object$comb.fixed, comb.random=object$comb.random,
        prediction=object$prediction,
        backtransf=object$backtransf,
	pscale=object$pscale, irscale = object$irscale, irunit = object$irunit,
        bylab=object$bylab, print.byvar=object$print.byvar,
	byseparator=object$byseparator, bystud=FALSE,
	print.CMH=object$print.CMH, warn=object$warn, ...)

## S3 method for class 'summary.meta'
print(x, digits = .settings$digits,
        comb.fixed=x$comb.fixed, comb.random=x$comb.random,
        prediction=x$prediction,
        print.byvar=x$print.byvar, byseparator=x$byseparator,
	print.CMH=x$print.CMH,
        header=TRUE, backtransf=x$backtransf,
	pscale=x$pscale, irscale = x$irscale, irunit = x$irunit,
        bylab.nchar=35,
        digits.zval = .settings$digits.zval,
        digits.Q = .settings$digits.Q, digits.tau2 = .settings$digits.tau2,
        digits.H = .settings$digits.H, digits.I2 = .settings$digits.I2,
	warn.backtransf = FALSE,
        ...)

cilayout(bracket="[", separator="; ")

Arguments

x

An object of class meta, metabias, or summary.meta.

object

An object of class meta.

sortvar

An optional vector used to sort the individual studies (must be of same length as x$TE).

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.

prediction

A logical indicating whether a prediction interval should be printed.

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.

header

A logical indicating whether information on title of meta-analysis, comparison and outcome should be printed at the beginning of the printout.

details

A logical indicating whether further details of individual studies should be printed.

ma

A logical indicating whether the summary results of the meta-analysis should be printed.

backtransf

A logical indicating whether printed results should be back transformed. 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.

bylab.nchar

A numeric specifying the number of characters to print from label for the grouping variable.

bystud

A logical indicating whether results of individual studies should be printed by grouping variable.

print.CMH

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

digits

Minimal number of significant digits, see print.default.

warn

A logical indicating whether the use of summary.meta in connection with metacum or metainf should result in a warning.

warn.backtransf

A logical indicating whether a warning should be printed if backtransformed proportions and rates are below 0 and backtransformed proportions are above 1.

bracket

A character with bracket symbol to print lower confidence interval: "[", "(", "{", "".

separator

A character string with information on separator between lower and upper confidence interval.

digits.se

Minimal number of significant digits for standard deviations and standard errors, see print.default.

digits.zval

Minimal number of significant digits for z- or t-value, see print.default.

digits.Q

Minimal number of significant digits for heterogeneity statistic Q, see print.default.

digits.tau2

Minimal number of significant digits for between-study variance, see print.default.

digits.H

Minimal number of significant digits for H statistic, see print.default.

digits.I2

Minimal number of significant digits for I-squared statistic, see print.default.

digits.prop

Minimal number of significant digits for proportions, see print.default.

digits.weight

Minimal number of significant digits for weights, see print.default.

...

Additional arguments.

Details

Note, in R package meta, version 3.0-0 some arguments have been removed from R functions summary.meta (arguments: byvar, level, level.comb, level.prediction) and print.summary.meta (arguments: level, level.comb, level.prediction). This functionality is now provided by R function update.meta (or directly in R functions metabin, metacont, metagen, metacor, and metaprop).

Review Manager 5 (RevMan 5) is the current software used for preparing and maintaining Cochrane Reviews (http://tech.cochrane.org/revman/). In RevMan 5, subgroup analyses can be defined and data from a Cochrane review can be imported to R using the function read.rm5. If a meta-analysis is then conducted using function metacr, information on subgroups is available in R (components byvar, bylab, and print.byvar, byvar in an object of class "meta"). Accordingly, by using function metacr there is no need to define subgroups in order to redo the statistical analysis conducted in the Cochrane review.

Note, for an object of type metaprop, starting with version 3.7-0 of meta, list elements TE, lower and upper in element study correspond to transformed proportions and confidence limits (regardless whether exact confidence limits are calculated; argument ciexact=TRUE in metaprop function). Accordingly, the following results are based on the same transformation defined by argument sm: list elements TE, lower and upper in elements study, fixed, random, within.fixed and within.random.

R function cilayout can be utilised to change the layout to print confidence intervals (both in printout from print.meta and print.summary.meta function as well as in forest plots). The default layout is "[lower; upper]". Another popular layout is "(lower - upper)" which is used throughout an R session by using R command cilayout("(", " - ").

Argument pscale can be used to rescale proportions, e.g. pscale=1000 means that proportions are expressed as events per 1000 observations. This is useful in situations with (very) low event probabilities.

Value

A list is returned by the function summary.meta with the following elements:

study

Results for individual studies (a list with elements TE, seTE, lower, upper, z, p, level, df).

fixed

Results for fixed effect model (a list with elements TE, seTE, lower, upper, z, p, level, df).

random

Results for random effects model (a list with elements TE, seTE, lower, upper, z, p, level, df).

k

Number of studies combined in meta-analysis.

Q

Heterogeneity statistic Q.

tau

Square-root of between-study variance.

se.tau

Standard error of square-root of between-study variance.

C

Scaling factor utilised internally to calculate common tau-squared across subgroups.

H

Heterogeneity statistic H (a list with elements TE, lower, upper).

I2

Heterogeneity statistic I2 (a list with elements TE, lower, upper), see Higgins & Thompson (2002).

k.all

Total number of studies.

Q.CMH

Cochran-Mantel-Haenszel test statistic for overall effect.

sm

A character string indicating underlying summary measure.

method

A character string with the pooling method.

call

Function call.

ci.lab

Label for confidence interval.

hakn

A logical indicating whether method by Hartung and Knapp was used.

method.tau

A character string indicating which method is used to estimate the between-study variance tau-squared.

tau.common

A logical indicating whether tau-squared is assumed to be the same across subgroups.

within.fixed

Result for fixed effect model within groups (a list with elements TE, seTE, lower, upper, z, p, level, df, harmonic.mean) - if byvar is not missing.

within.random

Result for random effects model within groups (a list with elements TE, seTE, lower, upper, z, p, level, df, harmonic.mean) - if byvar is not missing.

k.w

Number of studies combined within groups - if byvar is not missing.

Q.w

Heterogeneity statistic Q within groups - if byvar is not missing.

Q.b.fixed

Heterogeneity statistic Q between groups (based on fixed effect model) - if byvar is not missing.

Q.b.random

Heterogeneity statistic Q between groups (based on random effects model) - if byvar is not missing.

tau.w

Square-root of between-study variance within subgroups - if byvar is not missing.

C.w

Scaling factor utilised internally to calculate common tau-squared across subgroups.

H.w

Heterogeneity statistic H within subgroups (a list with elements TE, lower, upper) - if byvar is not missing.

I2.w

Heterogeneity statistic I2 within subgroups (a list with elements TE, lower, upper) - if byvar is not missing.

bylevs

Levels of grouping variable - if byvar is not missing.

title

Title of meta-analysis / systematic review.

complab

Comparison label.

outclab

Outcome label.

data

Original data (set) used to create meta object.

subset

Information on subset of original data used in meta-analysis.

prediction, level.predict
comb.fixed, comb.random, print.CMH

As defined above.

version

Version of R package meta used to create object.

Author(s)

Guido Schwarzer sc@imbi.uni-freiburg.de

References

Cooper H & Hedges LV (1994), The Handbook of Research Synthesis. Newbury Park, CA: Russell Sage Foundation.

Higgins JPT & Thompson SG (2002), Quantifying heterogeneity in a meta-analysis. Statistics in Medicine, 21, 1539–1558.

See Also

update.meta, metabin, metacont, metagen

Examples

1
2
3
4
5
6
7
8
9
data(Fleiss93cont)
meta1 <- metacont(n.e, mean.e, sd.e, n.c, mean.c, sd.c,
                  data=Fleiss93cont, sm="SMD",
                  studlab=paste(study, year))
summary(meta1)

summary(update(meta1, byvar=c(1,2,1,1,2), bylab="group"))

forest(update(meta1, byvar=c(1,2,1,1,2), bylab="group"))

Want to suggest features or report bugs for rdrr.io? Use the GitHub issue tracker.