General Package for Meta-Analysis

User-friendly general package providing standard methods for meta-analysis and supporting Schwarzer, Carpenter, and Rücker , "Meta-Analysis with R" (2015): - fixed effect and random effects meta-analysis; - several plots (forest, funnel, Galbraith / radial, L'Abbe, Baujat, bubble); - statistical tests and trim-and-fill method to evaluate bias in meta-analysis; - import data from 'RevMan 5'; - prediction interval, Hartung-Knapp and Paule-Mandel method for random effects model; - cumulative meta-analysis and leave-one-out meta-analysis; - meta-regression (if R package 'metafor' is installed); - generalised linear mixed models (if R packages 'metafor', 'lme4', 'numDeriv', and 'BiasedUrn' are installed).


News

*** meta, version 4.7-0, 2016-12-16 ***

** Major changes **

  • Forest plots:

    • forest plots with RevMan 5 and JAMA layout
    • use of mathematical symbols for I^2, tau^2, etc.
    • individual study results can be omitted from forest plot (especially useful to only print subgroup results)
    • labels can be printed at top of forest plot
  • Measure of between-study heterogeneity added:

  • Default settings of meta-analysis methods specified via gs() instead of extracting elements of list .settings (which makes output of args() easier to read, e.g., args(metabin))

  • Version of suggested R package metafor must be at least 1.9-9 (due to change in arguments of rma.uni() and rma.glmm())

** User-visible changes **

  • forest.meta():

    • argument layout: . new layouts: "JAMA" to produce forest plots with JAMA style (see http://jamanetwork.com/journals/jama/pages/instructions-for-authors) . RevMan 5 layout extended
    • arguments can be specified without using grid::unit(): plotwidth, colgap, colgap.left, colgap.right, colgap.studlab, colgap.forest, colgap.forest.left, colgap.forest.right
    • new argument study.results to print (default) or omit individual study results from forest plot
    • new argument bottom.lr to change position of labels on left and right side of forest plot
    • new arguments col.label.right and col.label.left to change colour of labels on left and right side of forest plot
    • argument weight renamed to weight.study and new argument weight.subgroup added to specify whether plotted subgroup results should be of same or different size
    • new arguments print.Rb, print.Rb.ci, Rb.text for heterogeneity measure Rb
    • new arguments to control printing: digits.cor, digits.mean, digits.sd, digits.time, digits.zval
    • new argument print.subgroup.labels to print (default) or omit rows with subgroup label from forest plot
    • new argument type.subgroup to change plotting of subgroup results
    • argument addspace renamed to addrow
    • new argument addrow.subgroups to add a blank line between subgroup results
    • new argument addrow.overall to add a blank before meta-analysis results
    • new argument blanks to enhance printing of test statistics, heterogeneity measurs, and p-values
    • new argument colgap.studlab to specify space between column with study labels and subsequent column
    • new arguments to change width of column with study labels: . calcwidth.fixed (consider text for fixed effect model) . calcwidth.random (consider text for random effects model) . calcwidth.hetstat (consider text for heterogeneity measures) . calcwidth.tests (consider text for tests of effect or subgroup differences) (these arguments are especially useful if only study labels are printed on left side of forest plot)
    • new column "effect.ci" with estimated treatment effect and confidence interval in one column
    • unnecessary arguments removed: text.I2, text.tau2
  • metabin(), metacont(), metacor(), metacr(), metacum(), metagen(), metainc(), metainf(), metaprop(), metarate(), trimfill.default(), trimfill.meta():

    • new measure of between-study heterogeneity implemented (list elements Rb, lower.Rb, upper.Rb)
  • summary.meta():

    • new measure of between-study heterogeneity added (list element Rb.w)
  • print.meta(), print.summary.meta():

    • print heterogeneity measure Rb
  • metabias.meta(), metabias.default():

    • checks for arguments implemented
  • New function gs() to get default settings

  • forest.meta(), metabin(), metacont(), metacor(), metacr(), metagen(), metainc(), metaprop(), metarate(), print.meta(), print.summary.meta():

    • use gs() to define defaults for arguments in meta-analysis functions, e.g. gs("hakn") instead of .settings$hakn
  • metareg():

    • stop with an error if version of metafor package is below 1.9-9
  • metabin(), metainc(), metaprop(), metarate():

    • for GLMMs, stop with an error if version of metafor package is below 1.9-9
  • metabin():

    • bug fix, do not stop with an error if no double zero events are present in a dataset with at least one study with NA event counts
  • metareg():

    • bug fix, use of covariate 'x' does not result in an error
  • settings.meta():

    • general settings for RevMan 5 and JAMA implemented
    • function can be used to change the layout of confidence intervals using arguments CIbracket and CIseparator (these arguments can also be set using cilayout())
  • Several help pages updated, especially

    • forest.meta(), settings.meta(), meta-package()

** Internal changes **

  • metabin(), metainc(), metaprop(), metarate(), metareg():

    • use argument test instead of knha and tdist for calls of rma.uni() and rma.glmm(); change in R package metafor, version 1.9-9
  • subgroup():

    • new measure Rb of between-study heterogeneity implemented
  • is.installed.package():

    • new check of version number of R package
    • use requireNamespace() instead of installed.packages()
  • format.p():

    • for small p-values, print "p < 0.01" or "p < 0.001" instead of "p < 0.0001" if digits.pval is 2 or 3, respectively
    • new argument zero to print ".001" instead of "0.001", etc
  • meta-internal():

    • set defaults for new arguments: smrate, layout

*** meta, version 4.6-0, 2016-10-12 ***

** Major changes **

  • New function metarate() to conduct meta-analysis of single incidence rates

  • Peters' test for funnel plot asymmetry implemented for meta-analysis of single proportions

  • Meta-analysis of ratio of means added to metacont()

  • Justification of additional columns in forest plot can be specified individually for each additional column

  • Justification of additional columns in forest plot can be specified individually for each additional column

  • Calculation of Freeman-Tukey double arcsin transformation and backtransformation slightly changed in meta-analysis of single proportions

  • By default, do not print a warning if backtransformation for metaprop() and metarate() objects results in values below 0 or above 1 (only for proportions); note, respective values are set to 0 or 1

** User-visible changes **

  • help page with brief overview of meta package added

  • preferred citation of meta package in publications changed; see output of command 'citation("meta")'

  • forest.meta(), metagen(), print.meta(), print.summary.meta(), summary.meta(), trimfill.default(), trimfill.meta(), update.meta():

    • new arguments irscale and irunit for meta-analysis objects created with metarate()
  • settings.meta():

    • new arguments smrate for meta-analysis objects created with metarate()
  • funnel.meta(), funnel.default():

    • new argument pos.studlab to change position of study labels
  • forest.meta():

    • new arguments just.addcols.left and just.addcols.right to specify justification of additional columns on left and right side of forest plot
  • metacont():

    • meta-analysis for ratio of means implemented (argument sm = "ROM")
    • new argument backtransf (if argument sm = "ROM")
  • metaprop():

    • change in Freeman-Tukey double arcsin transformation only visible in printouts if argument backtransf = FALSE or if list elements TE, TE.fixed, and TE.random (as well as confidence intervals) are extracted from a metaprop object
  • print.summary.meta():

    • print correct results for subgroup analyses of metaprop objects with sm = "PFT" (bugfix in internal subgroup() function)
  • print.meta(), print.summary.meta():

    • new argument warn.backtransf to specify whether a warning should be printed if backtransformed proportions and rates are below 0 and backtransformed proportions are above 1
  • Help pages updated: forest.meta(), metabias.meta(), metabin(), metacont(), metacor(), metagen(), metainc(), metainf(), metaprop(), print.meta(), print.summary.meta(), summary.meta(), trimfill.default(), trimfill.meta(), update.meta()

** Internal changes **

  • New function asin2ir() to backtransform arcsine transformed incidence rates

  • backtransf(), catmeth(), metacum(), metainf(), subgroup(), xlab():

    • extension to handle meta-analysis objects created with metarate()
  • metaprop(), asin2p():

    • calculation of Freeman-Tukey double arcsin transformation changed such that sm = "PFT" and sm = "PAS" result in similar estimates (TE, TE.fixed, TE.random), i.e. values are multiplied by 0.5 for sm = "PFT"
  • subgroup():

    • bux fix in calculation of harmonic mean of sample sizes (for metaprop objects with sm = "PFT") and event times (for metarate objects with sm = "IRFT")

*** meta, version 4.5-0, 2016-08-17 ***

** Major changes **

  • New features in forest plots:

    • printing of columns on left side of forest plot can be omitted
    • total person time can be printed
    • text for fixed effect and random effects model can be omitted from calculation of width for study labels
    • plot type for confidence intervals (square or diamond) can be specified for each study as well as fixed effect and random effects estimate
    • printing of test for treatment effect in subgroups possible
  • New function weights.meta() to calculate absolute and percentage weights in meta-analysis

  • New argument byseparator to define the separator between label and subgroup levels which is printed in meta-analysis summaries and forest plots - considered in all R functions dealing with meta-analysis and subgroups

  • Argument pscale - a scaling factor for printing of single event probabilities - considered in all R functions for single proportions; before this update, the pscale argument was only available in forest.meta()

** User-visible changes **

  • forest.meta():

    • argument ref considered for metaprop objects
    • argument leftcols = FALSE omits printing of columns on left side of forest plot
    • new argument pooled.times to print total person time
    • new argument calcwidth.pooled to include or exclude text from pooled estimates to determine width of study labels
    • the following arguments have been renamed (old arguments can still be used at the moment, however, will result in an informative warning message):
      . col.i -> col.study . col.i.inside.square -> col.inside . col.diamond.fixed.lines -> col.diamond.lines.fixed . col.diamond.random.lines -> col.diamond.lines.random
    • new arguments: . type.study, type.fixed, type.random (use squares or diamonds to plot treatment effects and confidence intervals) . col.inside.fixed, col.inside.random (colour to print confidence interval inside square) . test.effect.subgroup, test.effect.subgroup.fixed, test.effect.subgroup.random, label.test.effect.subgroup.fixed, label.test.effect.subgroup.random, fs.test.effect.subgroup, ff.test.effect.subgroup (print results for test of treatment effect in subgroups)
    • bug fix: reference line and lines for fixed effect and random effects estimate were too short if test.overall is TRUE
    • bug fix: arguments lab.e.attach.to.col and lab.c.attach.to.col were ignored for R objects created with metagen()
  • metabin(), metacont(), metacor(), metagen(), metainc(), metaprop(), forest.meta(), print.summary.meta(), summary.meta(), update.meta(), settings.meta():

    • new argument byseparator
  • metagen(), metaprop(), print.meta(), print.summary.meta(), summary.meta(), trimfill.meta(), trimfill.default(), update.meta():

    • new argument pscale
  • labbe.metabin(), labbe.default():

    • transformed event probabilites can be plotted, e.g., log odds event probabilities for odds ratio as summary measure (see argument backtransf)
    • line for null effect added by default (see arguments nulleffect, lwd.nulleffect, col.nulleffect)
  • metabin(), metainc(), metaprop():

    • use predict.rma() from metafor package to calculate prediction interval for GLMM method
    • print note for GLMM method that continuity correction is only used to calculate individual study results
  • Help pages updated: labbe.metabin(), labbe.default(), forest.meta(), metabin(), metacont(), metacor(), metagen(), metainc(), metaprop(), print.meta(), print.summary.meta(), summary.meta(), trimfill.meta(), trimfill.default(), update.meta()

** Internal changes **

  • New function bylabel() to print subgroup labels

  • update.meta():

    • do not consider columns 'n.e' and 'n.c' as sample sizes for metagen or metainc object if not used in original call of metagen() or metainc()
  • catmeth(), xlab():

    • new argument pscale
  • catmeth():

    • for GLMM, print information that continuity correction is only used to calculate individual study results
  • metacum(), metainf():

    • list object pscale added
  • metabin():

    • list objects incr.e and incr.c contains zeros for Peto method
    • print warning that no continuity correction is used for Peto method if any of the following arguments is used: incr, allincr, addincr, allstudies
  • metacr():

    • keep dataset used to conduct meta-analysis in list object data
  • paulemandel():

    • bug fix such that function does not result in an error if used with a single study
  • settings.meta():

    • bug fix such that use of argument method.tau works as expected

*** meta, version 4.4-1, 2016-06-20 ***

** User-visible changes **

  • metareg(), update.meta():
    • bug fix such that use of these functions with metaprop objects using argument method = "GLMM" does not result in an error

*** meta, version 4.4-0, 2016-05-13 ***

** Major changes **

  • Generalised linear mixed models (GLMMs) implemented by internal call of rma.glmm() from R package metafor by Wolfgang Viechtbauer

  • R packages lme4, numDeriv, and BiasedUrn added to suggested packages which are required by rma.glmm()

  • Print layout (especially number of printed digits) slightly modified which impacts output from print.meta(), print.summary.meta(), and forest.meta()

  • New arguments to change number of digits in printouts and forest plots

** User-visible changes **

  • metabin(), metainc(), metaprop():

    • extension for meta-analysis based on GLMM; see method argument and model.glmm argument (not used in metaprop function)
    • new argument ... to provide additional arguments to rma.glmm()
    • some arguments can be used for other meta-analysis methods than inverse variance method: method.tau, hakn, tau.common(), TE.tau(), tau.preset() () not considered for GLMMs
  • metabin():

    • do not print warning that inverse variance instead of Mantel-Haenszel method is used for analysis of a single study
    • print warning if continuity correction (arguments incr, allincr, addincr, allstudies) is used with arcsine difference, Peto method, or GLMM
    • check whether R package BiasedUrn is installed for conditional hypergeometric-normal GLMM (method = "GLMM", model.glmm = "CM.EL")
  • forest.meta():

    • extension to plot meta-analysis based on GLMM
    • labels argument can be used instead of label argument to change labels on x-axis (axis() uses labels argument)
  • funnel.meta():

    • print default labels on y-axis with capital first letter
  • metareg() and update.meta():

    • extension for meta-analysis based on GLMM
  • print.meta():

    • new arguments to control printing: digits.se, digits.zval, digits.Q, digits.tau2, digits.H, digits.I2, digits.prop, digits.weight
    • argument ... passed on to internal call of print.summary.meta()
  • print.summary.meta():

    • new arguments to control printing: digits.zval, digits.Q, digits.tau2, digits.H, digits.I2
    • print "--" for missing z-value instead of "NA"
    • only print confidence interval for H and I2 if lower and upper limits are not NA
    • print Wald-type and Likelihood-Ratio heterogeneity test for GLMMs
  • settings.meta():

    • new arguments: model.glmm, digits, digits.se, digits.zval, digits.Q, digits.tau2, digits.H, digits.I2, digits.prop, digits.weight, digits.pval, digits.pval.Q
    • check whether R package metafor is installed for specific values of argument method.tau
    • check whether R packages required for GLMMs are available (if method = "GLMM"): metafor, lme4, numDeriv
  • Help pages updated: metabin(), metainc(), metaprop(), metareg(), forest(), print.meta(), print.summary.meta(), settings.meta(), update.meta()

** Internal changes **

  • New function:

    • format.NA() to print other text than "NA" for missing values
  • metagen():

    • only call paulemandel() if heterogeneity statistic Q is larger equal than number of studies minus 1 (otherwise between-study heterogeneity tau-squared is set equal to 0)
  • New list elements:

    • model.glmm, .glmm.fixed, .glmm.random, version.metafor in metabin(), metainc(), metaprop()
    • doublezeros in metabin() - only for odds ratio and risk ratio
    • allstudies, doublezeros, model.glmm, .glmm.fixed, .glmm.random, version.metafor in summary.meta()
  • meta-internal():

    • set defaults for new arguments: model.glmm, digits, digits.se, digits.zval, digits.Q, digits.tau2, digits.H, digits.I2, digits.prop, digits.weight, digits.pval, and digits.pval.Q
  • paulemandel():

    • more sensible warning if maximum number of iterations is reached
    • maximum number of iterations increased from 25 to 100
  • format.p():

    • print trailing zeros
  • catmeth():

    • print information for GLMMs
    • print information whether studies with double zeros are included in meta-analysis
  • is.installed.package():

    • new arguments for more flexible error and warning messages: func, argument, value, chksettings

2015-12-02, version 4.3-2

Function metacont:

  • bug fix such that correct treatment estimates for individual studies are calculated for Glass's delta (i.e. arguments sm = "SMD" and method.smd = "Glass")

Function metaprop:

  • print correct error message if number of events is larger than number of observations

2015-11-13, version 4.3-1

Function forest.meta:

  • new arguments 'digits.se', 'digits.tau2', 'digits.pval', 'digits.pval.Q', 'digits.Q', 'digits.I2' to control printing of standard errors, p-values, tau-squared and heterogeneity statistics
  • new arguments 'test.overall' and 'test.subgroup' controlling whether information on test for overall effect and heterogeneity should be printed

Internal function paulemandel:

  • bug fix such that studies with missing treatment effect and standard error get zero weight in random effects meta-analysis
  • do not stop estimation algorithm if estimated tau-squared is negative

Function settings.meta:

  • bug fix such that no error occurs if function is used with an unassigned argument

Internal functions format.p and format.tau:

  • new argument 'digits' to round p-values and tau-squared values

Internal functions chkchar, chkclass, chklength, chklevel, chklogical, chkmiss, chknull, chknumeric, setchar:

  • new argument 'name' to change name of checked argument in printout

Help page of R function forest.meta updated

2015-07-02, version 4.3-0

Functions metabin, metainc, and metaprop:

  • missing values are allowed in numbers of events or patients (studies with missing values get zero weight in meta-analysis)

Function forest.meta:

  • print information on test for overall effect (see arguments 'test.overall.fixed' and 'test.overall.random')
  • print information on test for subgroup differences in meta-analysis with subgroups (see arguments 'test.subgroup.fixed' and 'test.subgroup.random')
  • new argument 'layout' to change the layout of the forest plot
  • argument 'lab.NA' considered for all columns in forest plot (e.g. numbers of events and patients for metabin objects)
  • new argument 'lab.NA.effect' to label NAs in individual treatment estimates and confidence intervals
  • bug fix such that no error occurs if random effects estimate is missing

Function metareg:

  • additional arguments implemented (hakn, level.comb, intercept)
  • argument '...' is no longer ignored but passed on to R function rma.uni (e.g., to control the iterative estimation process)
  • bug fix such that a fixed effect meta-regression can be conducted (argument method.tau="FE")

Function metabin:

  • use Inverse Variance instead of Mantel-Haenszel method if only a single study has a non-missing treatment estimate or standard error

Functions settings.meta and meta-internal:

  • code added for new arguments in forest.meta function to print information on tests

Help pages:

  • help page of R functions metareg and forest.meta updated
  • link to RevMan webpage updated

2015-05-08, version 4.2-0

Copyright changed (new names for Institute and Medical Center)

Function metacont:

  • new argument 'exact.smd' to implement exact formulae for Hedges' g and Cohen's d (White and Thomas, 2005; Hedges, 1981)
  • use formula from Borenstein et al. (2009) to calculate standard error for Cohen's d

Function forest.meta:

  • bug fix such that additional columns used in arguments leftcols and rightcols are sorted appropriately if argument sortvar is not missing
  • prediction interval can be printed if random effects estimate is not shown
  • new argument print.I2.ci to print confidence intervals for I-squared

Function print.meta and print.summary.meta:

  • prediction interval can be printed if random effects estimate is not shown

Functions settings.meta, meta-internal, catmeth and update.meta:

  • code added for new argument 'exact.smd' in metacont function

Functions ci and kentau:

  • calculate p-values without floating point number representation problems, e.g. the command ci(9, 1) does not result in a p-value of 0 but 2.257177e-19

Several help pages updated

  • reflect changes in metacont function
  • updated RevMan 5 reference

2015-02-04, version 4.1-0

Title of R package changed.

Function metacont:

  • new argument 'method.smd' to implement Cohen's d (method.smd="Cohen") and Glass' delta (method.smd="Glass") as additional effect measures for the standardised mean difference (sm="SMD")
  • new argument 'sd.glass' to choose the denominator for Glass' delta

Function update.meta:

  • new arguments 'method.smd' and 'sd.glass' added

Function summary.meta:

  • information for new arguments 'method.smd' and 'sd.glass' added to summary.meta object

Functions settings.meta and meta-internal:

  • code added for new arguments 'method.smd' and 'sd.glass' in metacont function

Function forest.meta:

  • bug fix such that using this function with a metaprop object and subgroups will not result in staggered point estimates

Function metagen:

  • bug fix such that studies with missing treatment effect (argument TE) but available standard error (argument seTE) get zero weight in meta-analysis

Function paulemandel (used internally):

  • only consider studies without missing treatment effect (argument TE) and standard error (argument seTE) in calculation of between-study variance tau-squared

Function chklevel (used internally):

  • print meaningful error message if confidence limit is outside the range (0, 1)

Function catmeth (used internally):

  • print information on method to estimate the standardised mean difference used in metacont function

Help pages of metacont and update.meta functions updated

2015-01-06, version 4.0-3

Function metabin:

  • bug fix such that printing an R object created using the Mantel-Haenszel and Peto method does not result in an error if any study has zero events in both groups

2014-12-06, version 4.0-2

Function metabin:

  • bug fix such that use of Peto method does not result in an error
  • argument 'sm="ASD"' for arcsine difference instead of 'sm="AS"' (abbreviations 'sm="AS"' and 'sm="A"' can be used as well)

Functions metabin, metacont, metacor, metagen, metainc, and metaprop:

  • Weights w.random.w are calculated from random effects meta-analysis ignoring subgroup membership (internally used function subgroup changed accordingly)
  • for subgroup analysis, argument 'tau.common' is set to TRUE if argument tau.preset is not NULL

2014-11-19, version 4.0-1

Function forest.meta:

  • bug fix such that function can be used with subgroups and additional columns (arguments leftcols and rightcols)

2014-11-19, version 4.0-0

Major revision

This update has been declared as major revision as R code to conduct subgroup analyses has been moved from R functions summary.meta and forest.meta to R functions metabin, metacont, metacor, metagen, metainc, and metaprop. Accordingly, an R object generated with these functions contains all results from subgroup analyses (see corresponding help pages).

In the case of subgroups, the overall treatment effect in fixed effect and random effects meta-analysis ignores subgroup membership. See Borenstein et al. (2011), Introduction to Meta-Analysis, Wiley, Chapter 19, "Obtaining an overall effect in the presence of subgroups, Option 3.

Furthermore, several checks of function arguments have been implented in version 4.0-0 of meta.

Function addvar has been removed from R package meta (remaining functionality provided by forest.meta function)

Function forest.meta:

  • new meaning for argument 'just' which determines the justification of all columns but study labels (argument 'just.studlab') and columns added to the forest plot (argument 'just.addcols')
  • new argument 'just.addcols' to change justification of text in additional columns
  • new arguments 'text.I2' and 'text.tau2'
  • for metaprop objects, values "n" and "event" handled as standard columns in argument 'rightcols' and 'leftcols', i.e. justification is determined by argument 'just.cols'
  • subgroup results printed with the same polygon height as overall results, i.e. percentage weight is not considered to determine polygon height for subgroups

Function bubble.metareg:

  • bug fix such that bubble plot is generated for meta-regression objects without intercept
  • bug fix such that use of function does not result in an error for some effect measures, e.g. sm="RR", "OR", or "HR"

New R functions (used internally):

  • subgroup, hetcalc
  • updateversion
  • bylevs, byvarname
  • chkchar, chkclass, chklength, chklevel, chklogical, chkmetafor chkmiss, chknull, chknumeric
  • int2num, npn
  • setchar, setstudlab

Functions format.p, format.tau, catmeth, and print.summary.meta:

  • consider settings for option 'OutDec' (character used as decimal point in output conversions), e.g. options(OutDec=",") will print "1,0" instead of "1.0"

Functions print.summary.meta:

  • remove code for R objects created with version 2.0-0 or lower of meta
  • print 'p-value' instead of 'p.value'

Functions print.meta:

  • print 'p-value' instead of 'p.value'

Several help pages updated.

2014-09-12, version 3.8-0

Functions forest.meta, funnel.default, funnel.meta, metabin, metacor, metacr, metagen, metainc, metaprop, print.meta, print.summary.meta, summary.meta, trimfill.default, trimfill.meta:

  • new argument 'backtransf' indicating whether effect measures should be back transformed

Functions print.meta, print.summary.meta:

  • argument 'logscale' removed (replaced by argument 'backtransf')

Functions print.summary.meta, forest.meta:

  • print prediction interval for Freeman-Tukey double arcsin transformation (sm="PFT", see help page on metaprop command)

Function forest.meta:

  • consider prediction interval to calculate limits on x-axis (if argument 'prediction=TRUE')

Function bubble.metareg:

  • new argument 'regline' indicating whether regression line should be added to plot

Function settings.meta:

  • new argument 'print=TRUE' to print listing of all settings (function call without arguments does not print all settings any longer)
  • a list with previous settings can be provided (see help page)

New functions (used internally):

  • backtransf (for back transformation of effect measures)
  • is.relative.effect (check for relative effect measures)

File DESCRIPTION:

  • R package grid defined as Imports instead of Depends

Help pages

  • updated to reflect changes in version 3.8-0

2014-07-29, version 3.7-1

Function forest.meta:

  • bug fix such that lower and upper confidence interval limits will be sorted correctly if argument 'sortvar' is used (this bug has been introduced in version 3.7-0 of meta)
  • argument 'sortvar' works without reference to meta object, e.g. command forest(meta1, sortvar=TE) can be used instead of forest(meta1, sortvar=m1$TE) - see help page for examples.

Help page of forest.meta function:

  • examples using argument 'sortvar' added

2014-07-11, version 3.7-0

Function metaprop:

  • new argument 'method.ci' to implement various methods to calculate confidence intervals for individual studies (default: Clopper-Pearson method which is also called 'exact' binomial method)
  • list elements zval.fixed, pval.fixed, zval.random, pval.random set to NA

New functions:

  • ciWilsonScore (used internally in metaprop function)
  • ciAgrestiCoull (used internally in metaprop function)
  • ciSimpleAsymptotic (used internally in metaprop function)
  • estimate.missing (used internally in trimfill.default and trimfill.meta; so far function was defined in both trimfill functions)

Function metacont:

  • new argument 'pooledvar' to conduct meta-analysis of mean differences (sm="MD") based on pooled variance for individual studies

Function update.meta:

  • function can be used to upgrade R objects created with older versions of meta, i.e. all versions between 0.5 and 3.6-0
  • extended to objects of the following classes:
    • trimfill (fully functional)
    • metacum (only upgrade to current version of meta)
    • metainf (only upgrade to current version of meta)
  • new arguments:
    • method.ci (for metaprop objects)
    • pooledvar (for metacont objects)
    • left (for trimfill objects)
    • ma.fixed (for trimfill objects)
    • type (for trimfill objects)
    • n.iter.max (for trimfill objects)
  • new list element 'call.object', i.e call used to generate object used as input to update.meta function

Function as.data.frame.meta, baujat.meta, forest.meta, funnel.meta, labbe.metabin, metacum, metainf, print.meta, summary.meta, trimfill.meta:

  • call update.meta function for meta objects created with older meta packages (version < 3.7)

Functions metabin, metacont, metacor, metagen, metainc, metaprop, trimfill.default, trimfill.meta:

  • new list elements: lower, upper, zval, pval (i.e. calculate confidence limits as well as z- and p-values for individual studies)

Function print.meta and print.summary.meta:

  • print information on method used for confidence intervals of individual studies for metaprop objects

Functions metacum and metainf:

  • add calculations for metainc objects
  • new list element 'call' with function call
  • consider argument 'pooledvar' for metacont objects

Functions metabin, metacont, metacor, metagen, metainc, metaprop:

  • study labels will only be converted to characters for factor variables

Help pages

  • updated to reflect changes in version 3.7-0
  • argument tau.preset correctly described as the square-root of the between-study variance

2013-05-27, version 3.6.0

New functions:

  • baujat and baujat.meta (Baujat plot to explore heterogeneity in meta-analysis)
  • bubble and bubble.metareg (bubble plot to display the result of a meta-regression)

Function metareg:

  • class 'metareg' added
  • new list element .meta which is a list with information on meta-analysis object used in function call

Function update.meta:

  • argument 'studlab' fully functional (I missed this argument in version 3.2-0)

Function print.meta:

  • print study label for a single study in meta-analysis if argument 'details=TRUE' (internally function data.frame instead of cbind used)

New function is.installed.package (used internally)

  • replacement for function is.installed.metafor

Help pages datasets amlodipine and cisapride:

  • execute examples for Hartung-Knapp method

Help pages merged for the following commands:

  • forest and forest.meta
  • funnel and funnel.meta
  • labbe and labbe.metabin
  • metabias and metabias.meta
  • trimfill and trimfill.meta

2014-05-14, version 3.5-1

Function metabin:

  • Inverse variance method used instead of Mantel-Haenszel method if argument 'tau.common' is TRUE

Function metareg:

  • tilde sign not necessary in argument 'formula' to make this function more user friendly

Function forest.meta:

  • print common tau-squared for subgroups if argument tau.common is TRUE in meta-analysis object

Function metagen:

  • arguments 'n.e' and 'n.c' can be part of the dataset provided in argument 'data'
  • DerSimonian-Laird method used instead of Paule-Mandel method if argument 'tau.common' is TRUE

Functions metacor, metainc, and metaprop:

  • arguments title, complab, and outclab part of R object

Some help pages (slightly) updated.

2014-04-19, version 3.5-0

New R function settings.meta to define and print default settings for meta-analyses in R package meta

Function metagen:

  • Hartung and Knapp method added (previously the rma.uni function from R package metafor has been called for this method)
  • Paule-Mandel method to estimate between-study variance implemented using new internal function paulemandel which is based on R function mpaule.default from R package metRology from S.L.R. Ellison <s.ellison at lgc.co.uk> (Author of R function mpaule.default is S. Cowen <simon.cowen at lgc.co.uk> with amendments by S.L.R. Ellison)

Function metacont:

  • studies with missing treatment estimate get zero weight in meta-analysis

Functions metabin, metacont, metacor, metacr, metagen, metainc, metaprop:

  • default values changed according to R function settings.meta

Function metareg:

  • use argument method.tau="REML" if this argument is equal to "PM" for meta-analysis object

Several help pages updated.

2014-03-26, version 3.2-1

Function forest.meta:

  • bug fix such that correct confidence limits for individual studies will be printed if argument 'level' in function metabin etc. is not equal to the default 0.95. (this bug has been introduced in version 3.0-0 of meta)

2014-03-12, version 3.2-0

Functions metabin, metacont, metacor, metagen, metainc, metaprop:

  • heterogeneity statistics I-squared and H added to R object
  • column names changed in list object data (columns starting with a "." are used internally in update.meta function)
  • internally, string "byvar" is used as default label for grouping variable if argument bylab is not provided.

Function metareg:

  • internally variable .byvar used instead of byvar to reflect change in list object data (see above)

Function update.meta:

  • arguments 'byvar' and 'subset' fully functional
  • internally variables .TE (etc) used instead of TE (etc) to reflect change in list object data (see above)

Functions trimfill.default and trimfill.meta:

  • heterogeneity statistics I-squared and H added to R object

Function metagen:

  • bug fix such that weights (w.fixed, w.random) are calculated correctly if any standard error is missing or zero for Hartung-Knapp method (argument hakn=TRUE) or not using the DerSimonian Laird method (argument method.tau not equal to "DL")

Function summary.meta:

  • implement subgroup analysis for metainc objects
  • only (re)calculate heterogeneity statistics (Q, tau-squared, I-squared) for R objects generated with older versions of R package meta

Function forest.meta:

  • groups will not be sorted automatically in alphabetical order (new argument 'bysort'). Use argument bysort=FALSE, in order to get the old behaviour of forest.meta function.
  • only (re)calculate heterogeneity statistics (Q, tau-squared, I-squared) for R objects generated with older versions of R package meta

Function catmeth (used internally)

  • new argument 'tau.preset' to print information if between-study variance was pre-specified

Function print.meta and print.summary.meta

  • argument 'tau.preset' used in call to function catmeth

New internally used functions isquared and calcH

Some help pages updated

2013-12-01, version 3.1-2

Function forest.meta:

  • bug fix such that forest plot with subgroups will not result in an error for any meta object besides metaprop objects (this bug has been introduced in version 3.1-1 of meta)

2013-11-19, version 3.1-1

Function forest.meta:

  • bug fix such that random effects estimate will be printed for subgroups for metaprop objects using summary measure "PFT"

2013-11-11, version 3.1-0

New R function metainc (meta-analysis of incidence rates)

Continuity correction:

  • R functions metabin and metaprop do no longer print a warning in case of studies with a zero cell frequency
  • instead information on continuity correction is given under "Details on meta-analytical method" if a corresponding meta object is printed

Functions forest.meta, funnel.default, funnel.meta, print.meta, print.summary.meta, update.meta, catmeth, xlab:

  • modified to properly handle R objects of class "metainc"

Function metaprop:

  • use correct variable names for 'event' and 'n' in list object data if R function metaprop is called without argument data

Function metabin:

  • inverse variance method (argument sm="Inverse") is used automatically if argument tau.common is TRUE
  • bug fix such that call of R function metabin will not result in an error if argument tau.common is TRUE and method is equal to "MH" (Mantel-Haenszel method)

Function catmeth (used internally in R function print.summmary.meta):

  • print information on continuity correction for objects of class metabin, metaprop, and metainc

Function summary.meta:

  • modified such that fixed effect and random effects estimates and confidence intervals are only (re)calculated for very old versions of R package meta (version number < 2.x-x) if argument level.comb has not been used

Functions trimfill.meta and trimfill.default:

  • new list components lower.fixed, upper.fixed, zval.fixed, pval.fixed, lower.random, upper.random, zval.random, pval.random added to trimfill R object (should/could have been part of exported list since meta, version 2.0-0)

New datasets smoking and lungcancer (example datasets for R function metainc)

2013-09-17, version 3.0-1

Major revision

This update has been declared as major revision as the user interface has been changed by dropping arguments for the following functions:

  • print.meta (arguments level, level.comb, level.prediction removed)
  • summary.meta (byvar, level, level.comb, level.prediction)
  • metainf (level.comb)
  • metacum (level.comb)
  • forest.meta (byvar, level, level.comb, level.predict) This functionality is now provided by R function update.meta - see help page of R function update.meta for further details.

New function update.meta

  • update an existing meta object which was created with R function metabin, metacont, metagen, metaprop, or metacor

New function cilayout

  • change layout to print confidence intervals (in printout from R functions print.meta, print.summary.meta, and forest.meta)

Deprecated function plot.meta removed from R package meta

Functions metabin, metacont, metagen, metaprop, metacor:

  • code cleaning (in preparation for R function update.meta)
  • new list components:
    • data (original data(set) used in function call)
    • subset (information on subset of original data used in meta-analysis)

Function summary.meta:

  • new list components:
    • data (original data(set) used in function call)
    • subset (information on subset of original data used in meta-analysis)

Functions metareg:

  • argument 'data' renamed to 'x'
  • first two arguments interchanged (which is now in line with other R functions from R package meta)
  • modified such that information on grouping variable (list element 'byvar') is utilised if argument 'formula' is missing
  • any column from original dataset (list component 'data' in metabin object (etc) can be used in meta-regression

Function trimfill.meta:

  • new defaults for arguments 'comb.fixed' and 'comb.random' (by default only random effects estimate calculated)
  • arguments 'sm' and 'studlab' removed (values have been overwritten internally anyway)
  • new list components (depending on class of meta object used in function call):
    • event.e, event.c, event (number of events)
    • n.e, n.c, n (number of observations)
    • mean.e, mean.c, sd.e, sd.c (Mean and standard deviation)
    • cor (correlation)
    • class.x (class of meta object used in function call)

Function trimfill.default:

  • new default for argument comb.fixed (by default only random effects estimate calculated)

Function metacr:

  • new list components for Peto O-E method:
    • event.e, n.e, event.c, n.c

Function metaprop:

  • new list component incr.event

Function forest.meta:

  • bug fix such that call of forest.meta function will not result in an error in the following setting: (i) effect measure is equal to RR, OR, or HR and (ii) argument label is not a logical value.

Function print.summary.meta:

  • modified such that "0" instead of "< 0.0001" is printed if between-study heterogeneity tau-squared is equal to 0

New function format.tau (used internally):

  • print "0" instead of "< 0.0001" if tau-squared is zero

Function p.ci (used internally):

  • new arguments bracket.left, separator, bracket.right for more flexible layouts to print confidence intervals (see also R function cilayout)

Several help pages updated.

2013-08-09, version 2.5-1

Function forest.meta:

  • new argument just.studlab to change justification of study labels

Function print.meta:

  • print correct information on method to calculate approximate confidence interval for 'metaprop' objects with a single study

Function trimfill.meta:

  • new list components title, complab, outclab, label.e, label.c, label.left, label.right which are utilised in other R functions to enhance printout (see information on version 2.0-0 of R package meta)

2013-07-25, version 2.5-0

Function metacr:

  • new arguments prediction and level.predict (prediction interval for a new study)
  • new argument tau.common (common tau-squared across subgroups)
  • new arguments level and level.comb (confidence interval for single study / meta-analysis)

Functions trimfill.meta and trimfill.default:

  • new arguments prediction and level.predict (prediction interval for a new study)

Function forest.meta:

  • modified such that heterogeneity statistics are only printed in forest plot if results for fixed effect and/or random effects model are plotted (new defaults for arguments print.I2, print.tau2, and print.pval.Q)

Functions metagen, metabin, metacont, metaprop, metacor:

  • modified such that list components comb.fixed, comb.random, and prediction are set to FALSE for a single study (no meta-analysis for a single study)

Functions print.meta, print.summary.meta:

  • new argument logscale which can be used to print results for summary measures 'RR', 'OR', 'HR', or 'PLN' on logarithmic scale

Update of several help pages.

2013-06-20, version 2.4-1

Function metaprop:

  • bug fix such that call of forest.meta function with metaprop object does not result in an error (bug was introduced with meta, version 2.4-0)
  • new list components incr, allincr, addincr added to metaprop R object (should have been part of exported list since meta, version 1.5-0)

Function print.meta:

  • new arguments prediction and level.predict to print prediction interval for a new study

Function print.summary.meta:

  • call of internal function asin2p using argument warn to only print warnings if result for fixed effect, random effects model or prediction interval are printed

Function forest.meta:

  • call of internal function asin2p using argument warn to only print warnings if result for fixed effect, random effects model or prediction interval are plotted

Function asin2p (used internally for metaprop objects):

  • new argument warn to only print a warning in certain situations (see comments on functions print.meta and forest.meta)

Help pages metabin, metacont, metacor, metacr, metagen, metaprop:

  • example to generate forest plot added

2013-06-17, version 2.4-0

Functions metagen, metabin, metacont, metaprop, metacor:

  • new arguments prediction and level.predict (prediction interval for a new study)
  • new argument tau.common (common tau-squared across subgroups)
  • help pages updated accordingly

Function metaprop:

  • new default summary measure (sm="PLOGIT")
  • argument freeman.tukey removed

Function summary.meta:

  • new arguments prediction and level.predict (prediction interval for a new study)
  • new list component tau.common considered internally (for objects of type metagen, metabin, metacont, metaprop, metacor)
  • modified such that correct values for list components incr, allincr, and addincr of metaprop object are considered in calculations

Function forest.meta:

  • modified such that prediction interval can be plotted (new arguments: prediction, level.predict, text.predict, col.predict, col.predict.lines, fs.predict, fs.predict.labels, ff.predict, ff.predict.labels)
  • modified such that correct values for list components incr, allincr, and addincr of metaprop object are considered in calculations
  • modified such that information on confidence limits is printed for pooled estimates if CI level is different from CI level for individual studies

Function print.summary.meta:

  • modified such that a prediction interval is printed if argument prediction is TRUE
  • new list component tau.common considered internally (for objects of type metagen, metabin, metacont, metaprop, metacor)

Function catmeth (only used internally):

  • print information if common tau-squared assumed across subgroups (argument tau.common)

2013-05-12, version 2.3-0

Function forest.meta:

  • modified such that fixed effect and random effects estimates and confidence intervals are only (re)calculated for very old versions of R package meta (version number < 2.x-x)

Functions metabin:

  • bug fix such that function call with arguments sm="RR" and allstudies=TRUE does not result in an error in meta-analyses with zero events in both groups

2013-03-20, version 2.2-1

Function forest.meta:

  • new argument lab.NA (default: lab.NA=".") to label NAs (in older version of R package meta the fixed label 'NA' was used)
  • modified such that arguments colgap.forest.left and colgap.forest.right are considered (instead of only colgap.forest)

Functions labbe.metabin and labbe.default:

  • bug fix such that function call does not result in an error if any event probability is equal to NA

Function format.p (only used internally):

  • bug fix such that function call does not result in an error if any NAs were provided in the first function argument

2013-03-12, version 2.2-0

Function metabin:

  • modified so that studies with all events in both groups will be included in meta-analysis by default (in older versions of R package meta these studies were only included if argument allstudies=TRUE)
  • modified so that the standard error is positive for studies with all events in both groups (see Hartung & Knapp (2001), Stat Med, equation (18))

Function forest.meta:

  • modified so that values provided by argument xlim will be printed on x-axis label for relative effect measures (i.e. argument sm is equal to "RR", "OR", or "HR")
  • internally calculated default values for arguments smlab.pos and xlab.pos changed such that they will always lie within plotting range

2012-11-29, version 2.1-4

Functions forest.meta, metacum, metainf and print.meta:

  • modified so that backtransformation of Freeman-Tukey Double arcsine transformation (argument sm='PFT' in function metaprop) is calculated correctly for objects of class 'metacum' and 'metainf'

Function asin2p:

  • modified so that values outside the admissible range are set to the boundary values (i.e. results in estimated probabilities of 0 or 1). A warning is printed in this case.

Help pages metacum and metainf:

  • new argument n.harmonic.mean documented

2012-11-20, version 2.1-3

Function forest.meta:

  • modified so that the function works for an object of class 'metacum' or 'metainf' and argument sm equal to 'PFT' which previously resulted in an error message 'Error in if (col$range[1] <= TE.fixed & TE.fixed <= col$range[2]) ...'

2012-10-25, version 2.1-2

Functions forest.meta, metacum, metainf, summary.meta:

  • modified so that the function works if argument 'method.tau' is different from the default which previously resulted in an error message 'Error in sqrt(W) %*% X : non-conformable arguments'

Function forest.meta:

  • argument 'byvar' uses corresponding list element from meta-analysis object as default

2012-08-12, version 2.1-1

Function summary.meta:

  • list element 'k0' added to returned object for trim-and-fill method

Function print.summary.meta:

  • print number of added studies for trim-and-fill method

2012-05-18, version 2.1-0

Functions trimfill.meta and trimfill.default:

  • arguments hakn and method.tau added

Functions metacum and metainf:

  • modified so that class 'trimfill' is added to object if function metacum or metainf is used on object of class 'trimfill'

Function catmeth, print.meta, print.summary.meta:

  • modified so that information on use of trim-and-fill method is printed

Functions metabias.meta:

  • modified so that an error message is printed if used with object of class 'metacum' or 'metainf'

Functions funnel.meta:

  • modified so that an error message is printed if used with object of class 'metacum' or 'metainf'
  • modified so that by default different plot symbols (argument pch) are used with object of class 'trimfill'

Function .onLoad:

  • modified so that version nummer of meta package is printed when library is loaded

Help pages trimfill.meta and trimfill.default:

  • arguments hakn and method.tau documented

Help page funnel.meta:

  • changed default for argument pch documented

2012-05-03, version 2.0-4

Function metaprop:

  • modified so that variance estimate for log- and logit-transformation (sm="PLN" and sm="PLOGIT") is based on Pettigrew et al. (1986).

Reference Pettigrew et al. (1986) has been added to the following help pages:

  • metabin, metaprop

2012-04-17, version 2.0-2

Function metaprop:

  • modified so that a warning is printed if any sample size (argument n) is smaller than 10 for Freeman-Tukey double arcsine transformation, i.e. sm="PFT"

2012-04-04, version 2.0-1

Functions metabin, metacont, metacor, metagen, metaprop:

  • modified so that these functions can be used with arguments subset and byvar of different length

2012-03-20, version 2.0-0

Major revision

R package meta linked to R package metafor to provide additional statistical methods, e.g. meta-regression and other estimates for tau-squared (REML, ...)

New functions:

  • metareg (meta-regression)
  • metabias (generic method for function metabias)
  • metabias.default (generic method for function metabias)
  • metabias.meta (generic method for function metabias)
  • metabias.rm5 (generic method for function metabias)
  • print.rm5 (generic method for rm5-object)
  • print.summary.rm5 (generic method for rm5-object)
  • summary.rm5 (generic method for rm5-object)
  • catmeth (function used internally)
  • crtitle (function used internally)
  • hypergeometric (function used internally)
  • is.installed.metafor (function used internally)
  • kentau (function used internally)
  • linregcore (function used internally)
  • p2logit (function used internally)

Functions metabin, metacont, metacor, metagen, metaprop:

  • new arguments:
    • hakn (Hartung-Knapp method)
    • method.tau (estimation method for tau-squared)
    • tau.preset (fixed value for tau)
    • TE.tau (pre-specified treatment effect to estimate tau)
    • method.bias (test for funnel plot asymmetry used in metabias)
    • label.left (Label on left side of forest plot, new argument in functions metabin, metacont, and metagen)
    • label.right (Label on right side of forest plot, new argument in functions metabin, metacont, and metagen)
    • warn (print warning messages, new argument in functions metacont and metagen)
  • new list components of returned object:
    • se.tau2 (standard error of tau-squared)
    • hakn (Hartung-Knapp method)
    • method.tau (estimation method for tau-squared)
    • tau.preset (fixed value for tau)
    • TE.tau (pre-specified treatment effect to estimate tau)
    • method.bias (test for funnel plot asymmetry used in metabias)
    • label.left (Label on left side of forst plot, new list component in functions metabin, metacont, and metagen)
    • label.right (Label on right side of forst plot, new list component in functions metabin, metacont, and metagen)
  • argument 'warn' suppresses more warning messages if FALSE
  • function metabin: studies are excluded from meta-analysis if (event.e > n.e | event.c > n.c) or (n.e <= 0 | n.c <= 0) or (event.e < 0 | event.c < 0)

Function metacum and metainf:

  • modified so that NULL is returned if function is used with a single study
  • modified so that new arguments hakn, method.tau, tau.preset, method.bias, label.left, label.right are considered in execution of the function
  • argument level removed

Function metaprop:

  • modified so that the correct variance function 1/(n+0.5) instead of 1/(n+1) is used for the Freeman-Tukey double arcsine transformation (i.e. sm="PFT") - see also news on function asin2p

Function asin2p:

  • completely rewritten as back transformation of Freeman-Tukey transformed proportions was inaccurate
  • back transformation of Freeman-Tukey proportions according to Miller (1978) - see help page of R command metaprop

Function print.metabias:

  • print a warning if number of studies is too small to conduct a test for funnel plot asymmetry (see new argument k.min)

Function print.summary.meta:

  • new argument bylab.nchar
  • print test for subgroup differences for both fixed effect and random effects model
  • value 'invisible(NULL)' returned for metacum and metainf objects

Function metacr:

  • new arguments:
    • sm (summary measure)
    • method (pooling method)
    • comb.fixed (fixed effect model)
    • comb.random (random effects model)
    • swap.events (only for binary data)
    • method.tau (estimation method for between-study variance)
    • hakn (Hartung-Knapp adjustment)
    • title (Title of Cochrane review)
    • complab (Comparison label)
    • outclab (Outcome label)
    • warn (print warning messages)
  • removed argument:
    • smother (summary measure)
  • value 'NULL' returned if no data is available for selection of comp.no and outcome.no

Function read.rm5:

  • changed substantially for reading of RevMan 5.1 files

Function summary.meta:

  • modified so that new arguments hakn, method.tau, tau.preset, method.bias are considered in execution of the function
  • argument 'warn' suppresses more warning messages

Function forest.meta:

  • modified so that the treatment effect and 95% confidence interval is printed in the correct order for objects of class metaprop if argument sort or order is used
  • symmetric forest plot by default (argument xlim="s")
  • new arguments:
    • smlab, smlab.pos, fs.smlab, fflab (Label for summary measure - at top of figure)
    • label.right, label.left, fs.lr, ff.lr (Label on right and left side)
    • overall.hetstat (heterogeneity information for overall effect)

Function funnel.default and funnel.meta:

  • modified so that arguments col.fixed and col.random are recognised

Function metabias.default and metabias.meta:

  • new argument k.min: test for funnel plot asymmetry only conducted if number of studies in meta-analysis is larger or equal to k.min
  • new argument '...' (ignored at the moment)

Function trimfill.default and trimfill.meta:

  • value 'invisible(NULL)' returned if number of studies is smaller than 3

New datasets: amlodipine, cisapride

File FLEISS93.MTV moved from directory data to directory extdata

Update of several help pages. Some new help pages added.

2010-10-28, version 1.6-1

Function forest.meta:

  • modified so that the number of events is printed in the correct order for objects of class metaprop if argument sort or order is used
  • modified so that transformed proportions are printed for individual studies in column 'TE' if function metagen is used with argument sm equal to either 'PLN', 'PLOGIT', 'PAS', or 'PFT'

Function as.data.frame.meta:

  • modified so that the function works for meta-analyses with six studies which previously resulted in an error message 'Error: evaluation nested too deeply: infinite recursion ...'
  • modified so that additional arguments '...' can be passed to function

Function addvar:

  • option stringsAsFactors=FALSE added to internal call of R function as.data.frame.meta
  • additional checks for existence of columns by.x and by.y
  • additional checks for situations with duplicate entries for columns by.x and by.y added

Function print.meta:

  • modified so that back-transformed proportions are printed for individual studies if function metagen is used with argument sm equal to either 'PLN', 'PLOGIT', 'PAS', or 'PFT'

Examples given in the following help pages have been (slightly) updated:

  • read.mtv, read.rm5, metacr

2010-06-21, version 1.6-0

Function forest.meta:

  • for subgroup analyses (i.e. groups defined by argument 'byvar'), result for both fixed effect and random effects model are printed (in older versions of the meta package only results for either fixed effect or random effects model could be printed)
  • new arguments text.fixed.w and text.random.w to specify label for estimates within subgroups
  • new arguments to change colour of several parts of the plot: col.i.inside.square, col.square, col.square.lines, col.diamond, col.diamond.fixed, col.diamond.random, col.diamond.lines, col.diamond.fixed.lines, col.diamond.random.lines
  • new arguments to print information on heterogeneity measures: print.I2, print.tau2, print.Q, print.pval.Q, hetstat, hetlab
  • new arguments to change fontsize and fontface of several parts of the plot: fs.heading, fs.fixed, fs.random, fs.study, fs.fixed.labels, fs.random.labels, fs.study.labels, fs.hetstat, fs.axis, fs.xlab, ff.heading, ff.fixed, ff.random, ff.study, ff.fixed.labels, ff.random.labels, ff.study.labels, ff.hetstat, ff.axis, ff.xlab
  • new arguments to change gap between columns colgap.left, colgap.right=colgap, colgap.forest, colgap.forest.left, colgap.forest.right
  • new argument 'just' to change justification of text for additional columns
  • new argument 'addspace' to print a blank line at top and bottom of study results
  • argument 'squaresize' supersedes argument 'boxsize'
  • new argument 'new' indicating whether a new figure should be printed in an existing graphics window (internally, the grid.newpage command is used if new=TRUE)
  • no line is printed for the fixed effect and random effects model if lty.fixed=NULL or lty.random=NULL, respectively
  • symmetric forest plots can be produced by setting argument xlim="s"

Function print.summary.meta:

  • new argument print.CMH indicating whether Cochran-Mantel-Haenszel test for overall effect should be printed (default print.CMH=FALSE)
  • For subgroup analyses (i.e. groups defined by argument 'byvar'), result for test of heterogeneity printed separately for fixed effect and random effects model

Functions metabin and summary.meta:

  • new argument print.CMH indicating whether Cochran-Mantel-Haenszel test for overall effect should be printed (default print.CMH=FALSE)

The following help pages have been updated:

  • forest.meta, metabin, print.summary.meta, summary.meta

2010-05-07, version 1.5-0

Version jump to 1.5-0 as several changes have been implemented.

New functions:

  • metacor (meta-analysis of correlations)
  • forest (generic method for forest plots)
  • forest.meta (generic method for forest plots)
  • radial (generic method for radial plots)
  • radial.default (generic method for radial plots)
  • radial.meta (generic method for radial plots)
  • asin2p (function used internally)
  • logit2p (function used internally)
  • xlab (function used internally)
  • z2cor (function used internally)

Functions forest.meta:

  • new arguments (pooled.totals, pooled.events) to specify whether total number of observations and events should be displayed in the plot
  • new argument (pscale) to rescale proportions for objects of class metaprop
  • modified so that argument label is recognised for other effect measures than RR, OR, and HR
  • modified so that argument xlim is recognised for other effect measures than RR, OR, and HR
  • arguments rightlabs and leftlabs accept NAs for columns using default labels
  • modified so that significant digits are printed uniformly
  • correct sum of percentage weight is printed for random effects model in forest plots with subgroups
  • x limits (min,max) of the plot are defined by the width of confidence intervals instead of (0,1) for objects of class metaprop

Function metaprop:

  • implementation of additional transformations: log transformation, logit transformation, raw, i.e. untransformed, proportions
  • new argument sm to choose summary measure (i.e. transformation)
  • use of argument freeman.tukey is deprecated (use argument sm instead)

Functions funnel and funnel.meta:

  • argument y removed

Functions labbe and labbe.meta:

  • argument y removed

Functions trimfill and trimfill.meta:

  • argument seTE removed

Function summary.meta:

  • new list objects H.w, I2.w, Q.b.fixed and Q.b.random for heterogeneity statistics within subgroups

Extension for meta-analysis of correlations:

  • forest.meta, metacum, metainf, print.meta, print.summary.meta, summary.meta

Function plot.meta:

  • a warning is printed that the function is no longer maintained (function forest.meta should be used instead)

New list element version with information on version number of meta package used to create an object (applies only to object creating functions, e.g. metabin, metabias).

Update of several help pages.

Use file NEWS instead of ChangeLog to document changes.

2010-01-12, version 1.1-8

Functions summary.meta, print.summary.meta:

  • modified so that a test for subgroup differences is not calculated and printed for meta-analyses using the Mantel-Haenszel method for binary data

2010-01-11, version 1.1-7

Functions metabin, metacont, metagen, metaprop:

  • modified so that a sensible default value is used for argument bylab if argument byvar is not missing

2010-01-11, version 1.1-6

Function forest:

  • modified so that additional columns are printed in the correct order if argument sort or order is used

2009-12-21, version 1.1-5

Function forest (incl. help page):

  • new argument digits specifying minimal number of significant digits for treatment estimate and its confidence interval

2009-11-04, version 1.1-4

Function summary.meta:

  • modified so that results for subgroups (if byvar != NULL) are calculated for both fixed effect and random effects model:
    • list 'within' no longer returned by function summary.meta
    • lists 'within.fixed' and 'within.random' returned by function summary.meta
  • modified so that variable name of subgroups is printed correctly
  • check whether input is an object of class summary.meta

Function print.summary.meta:

  • modified so that a warning is printed if both comb.fixed and comb.random are TRUE and results for subgroups are supposed to be printed

Help pages of functions print.summary.meta and forest updated:

  • detailed information on printing and plotting of subgroup results if both comb.fixed and comb.random are TRUE

Help page of function metagen updated:

  • new example with meta-analysis of survival data

2009-10-30, version 1.1-3

New functions trimfill, trimfill.default and trimfill.meta:

  • generic method for trim-and-fill method

2009-10-09, version 1.1-2

New functions labbe, labbe.default, labbe.metabin:

  • produce L'Abbe plots

New functions funnel, funnel.default and funnel.meta:

  • generic method for funnel plots

Functions funnel.default and funnel.meta:

  • modified so that contour-enhanced funnel plots can be produced (new arguments: contour.levels, col.contour, ref)
  • modified so that study labels can be printed on funnel plot (new arguments: studlab, cex.studlab)
  • modified so that line type, width and colour can be changed for fixed effect treatment effect (new arguments: lty.fixed, lwd.fixed, col.fixed)
  • modified so that random effects treatment effect can be plotted (new arguments: comb.random, lty.random, lwd.random, col.random)
  • new default values for arguments:
    • pch=21 (previously: pch=1)
    • comb.fixed=x$comb.fixed
  • modified so that background colour of points in funnel plot can be changed (new argument: bg)

Function forest:

  • new default values for arguments lab.e and lab.c: x$label.e and x$label.c, respectively. If these values are NULL the old default values "Experimental" and "Control" are used.

Functions metabin, metacont, metagen:

  • arguments label.e and label.c added

Function metacr:

  • use arguments label.e and label.c in calls to functions metabin, metacont, metagen

2009-08-31, version 1.0-6

First major version released on CRAN

No NEWS available for versions < 1.0

Reference manual

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install.packages("meta")

4.8-4 by Guido Schwarzer, 3 months ago


https://github.com/guido-s/meta http://meta-analysis-with-r.org


Browse source code at https://github.com/cran/meta


Authors: Guido Schwarzer [cre, aut]


Documentation:   PDF Manual  


Task views: Clinical Trial Design, Monitoring, and Analysis, Meta-Analysis


GPL (>= 2) license


Imports grid

Suggests metafor, lme4, numDeriv, BiasedUrn


Imported by gemtc.

Depended on by MultiPhen, metasens, netmeta.

Suggested by RcmdrPlugin.EZR, mvmeta, personograph.


See at CRAN