https://github.com/cran/meta
Tip revision: ff52fea72c192d08a00da704f4882a0f7ec5b14d authored by Guido Schwarzer on 29 January 2020, 20:20:02 UTC
version 4.10-0
version 4.10-0
Tip revision: ff52fea
NEWS
*** meta, version 4.10-0, 2020-01-29 ***
** Major changes **
* New function drapery() to generate a drapery plot
(based on p-value curves)
** Bug fixes **
* funnel.meta():
- print contours in contour-enhanced funnel plots at correct
position for relative effect measures (bug was introduced in
meta, version 4.9-8)
** User-visible changes **
* update.meta():
- do not print a warning concerning argument 'Q.Cochrane' if
argument sm = "ASD" for meta-analysis objects created with
metabin()
* print.summary.meta():
- do not print z- and p-values if test for an overall effect was
not conducted (see argument 'null.effect' in metamean(),
metaprop(), and metarate())
*** meta, version 4.9-9, 2019-12-19 ***
** Bug fixes **
* forest.meta():
- printing an additional column on the right side of the forest
plot does not result in an error (bug was introduced in meta,
version 4.9-8)
** User-visible changes **
* labbe():
- new argument 'pos.studlab'
- argument checks implemented
* baujat(), bubble():
- argument 'pos' renamed to 'pos.studlab'
- argument checks implemented
*** meta, version 4.9-8, 2019-12-16 ***
** Major changes **
* Confidence intervals for the between-study variance tau2 and its
square root tau are calculated
* Print tau as well as confidence intervals for tau2 and tau in
outputs
* Square root of between-study variance can be printed in forest
plots instead of between-study variance tau2; in addition, the
confidence interval for tau2 or tau can be printed
* Use R package metafor to estimate between-study variance tau2 for
DerSimonian-Laird and Paule-Mandel method (which has been already
used for all other methods to estimate tau2)
* For Mantel-Haenszel (MH) method, report results as MH method
(instead of inverse variance, IV) for meta-analysis of binary
outcome with a single study (results are identical for MH and IV
method in this situation)
* Number of studies printed without digits in forest plots for R
objects created with metabind()
* P-values can be printed according to JAMA reporting standards
* In subgroup analyses, print the group labels instead of levels if
the grouping variable is a factor
* In funnel plot, print funnel around random effects (instead of
fixed effect) estimate if only random effects meta-analysis is
conducted; only show funnel if either fixed effect or random
effects meta-analysis was conducted
* Change preferred citation of R package meta from Schwarzer (2007)
to Balduzzi et al. (2019), DOI: 10.1136/ebmental-2019-300117
** User-visible changes **
* print.summary.meta(), forest.meta():
- new argument 'JAMA.pval' to print p-values according to JAMA
reporting standards
* print.summary.meta():
- new argument 'zero.pval' to remove leading zeros from p-values
- print information on estimation of between-study variance even
if only results for fixed effect model is shown
- print information if Mantel-Haenszel estimate is used to
calculate Q and tau2 (implemented similar to RevMan 5)
- global setting for 'text.tau2' as defined in settings.meta() is
considered in details of meta-analytical method
* print.meta():
- do not print (missing) weights for GLMMs
* update.meta():
- by default, do not print warnings (argument 'warn')
- add information on variable defining subgroups (argument
'byvar') to meta-analysis dataset
* Command 'settings.meta("JAMA")' will change the settings for
arguments 'zero.pval' and 'JAMA.pval'
* Help page with description of R package updated
* Major update of other help pages:
metacont(), metacor(), and metamean()
** Internal changes **
* function paulemandel() removed from package as R package metafor
is used to estimate the between-study variance
* formatPT():
- new argument 'JAMA'
* List elements 'C' and 'C.w' (scaling factor to estimate common
between-study variance) removed from meta-analysis objects
* Import confint.rma.uni() from metafor to calculate confidence
intervals for tau2 and tau
* new internal function pasteCI() to print formatted CIs
* new internal function is.wholenumber() to check for whole numbers
*** meta, version 4.9-7, 2019-09-27 ***
** Major changes **
* Subgroup analysis using argument 'byvar' possible for generalised
linear mixed models (GLMMs)
** Bug fixes **
* metaprop():
- no error if argument 'tau.common' is TRUE for GLMM
* metabin(), metainc(), metarate():
- consider argument 'control' in subgroup analysis
** User-visible changes **
* Major update of help pages:
metabin(), metagen(), metainc(), metaprop(), and metarate()
*** meta, version 4.9-6, 2019-08-06 ***
** Major changes **
* New functions to calculate the number needed to treat from the
results of a meta-analysis
* Equivalence limits can be added to forest plots
* Font family can be specified in forest plots
* Print Wald-type test of heterogeneity for generalised linear mixed
models (problem fixed in R package metafor, version 2.1-0)
** Bug fixes **
* forest.meta():
- (always) print correct length for reference line
- (always) print label on x-axis at the correct vertical position
- (always) print graph labels on the left and right side of the
forest plot at the correct vertical position
- no error if additional numeric variable is added to the right
side of the forest plot (argument 'rightcols')
* summary.meta():
- consider argument 'bylab'
* metaprop():
- allow values 0 and 1 for argument 'null.effect'
** User-visible changes **
* forest.meta():
- new arguments 'lower.equi', 'upper.equi', 'lty.equi',
'col.equi', and 'fill.equi' to add equivalence limits
- new argument 'fontfamily' to specify the font family
* forest.metabind():
- information on heterogeneity printed for each meta-analysis
** Internal changes **
* ciAgrestiCoull():
- set lower confidence limit to 0 for negative values
- set upper confidence limit to 1 for values above 1
* subgroup meta-analyses return new list element 'pval.Q.w'
(change in internal function subgroup())
*** meta, version 4.9-5, 2019-04-11 ***
** Major changes **
* For the generic inverse variance method, treatment estimates and
standard errors of individual studies can be derived from
- p-value or confidence limits
- sample size, median, interquartile range and / or range
(Wan et al. (2014), BMC Med Res Meth, 14, 135)
* New functions for the conversion of effect measures:
- smd2or() - from standardised mean difference to log odds ratio
- or2smd() - from log odds ratio to standardised mean difference
* Harbord test for funnel plot asymmetry implemented for risk ratio
as effect measure
* Generalised linear mixed model is the new default method for
meta-analysis of single proportions using the logit transformation
* R packages metafor and lme4 moved from Suggests to Imports
* Suppress printing of Wald-type test of heterogeneity for
generalised linear mixed models (problem in R function rma.glmm()
from R package metafor, version 2.0-0)
* Use roxygen2 for development of R package meta
** User-visible changes **
* metagen():
- new arguments 'pval', 'df', 'lower', 'upper', 'level.ci',
'median', 'q1', 'q3', 'min', 'max', 'approx.TE', 'approx.seTE'
to approximate treatment estimates and / or standard errors from
other information
* forest.meta():
- printing of leading zeros in p-values can be suppressed (new
argument 'zero.pval')
- rounding of values for additional numerical columns possible
(new arguments 'digits.addcols', 'digits.addcols.left', and
'digits.addcols.right')
- argument 'big.mark' is considered for additional columns
- new arguments 'type.subgroup.fixed', 'type.subgroup.random', and
'lab.NA.weight'
* settings.meta() and gs():
- argument names can be abbreviated
* Major update of help pages of metagen() and metaprop()
** Bug fixes **
* metacum(), metainf():
- consider argument 'method' for meta-analysis objects created
with metaprop() or metarate()
* forest.meta():
- argument 'studlab' can be used with objects created with
metacum() or metainf()
* subgroup():
- return subgroup sample sizes for objects created with metagen()
** Internal changes **
* New internal functions TE.seTE.ci(), TE.seTE.iqr(),
TE.seTE.iqr.range(), TE.seTE.range(), and seTE.ci.pval() to
approximate treatment estimates and / or standard errors from other
information
* setchar():
- new argument 'stop.at.error'
* metagen():
- list element 'data' contains the dataset of the meta-analysis
object (i.e., list element 'data') instead of the whole
meta-analysis object
*** meta, version 4.9-4, 2019-01-02 ***
** Major changes **
* Information on residual heterogeneity in meta-analyses with
subgroups shown in printouts and forest plots
** User-visible changes **
* forest.meta():
- new arguments 'resid.hetstat' and 'resid.hetlab' to control
printing of information on residual heterogeneity in
meta-analyses with subgroups
** Bug fixes **
* forest.meta():
- works in meta-analyses with subgroups if argument 'allstudies'
is FALSE
*** meta, version 4.9-3, 2018-11-29 ***
** Major changes **
* New argument 'control' in meta-analysis functions which is passed
on to R function rma.uni() or rma.glmm() from R package metafor to
control the iterative process to estimate the between-study
variance tau^2
** User-visible changes **
* metabin(), metacont(), metacor(), metagen(), metainc(),
metamean(), metaprop(), metarate(), update.meta():
- new argument 'control' (see major changes)
* forest.meta():
- new argument 'calcwidth.subgroup'
** Bug fixes **
* bubble.metareg():
- ignore missing values in covariate to calculate limits on x-axis
- works if data set used to create meta-analysis object is a
tibble instead of a data frame
** Internal changes **
* metabind():
- argument 'tau.common' only considered for subgroup analyses
* hetcalc():
- argument 'control' passed on to R function rma.uni() from R
package metafor
* metacum(), metainf(), subgroup():
- argument 'control' from meta-analysis objects considered
*** meta, version 4.9-2, 2018-06-06 ***
** Major changes **
* All p-values of Q statistics are list elements of meta-analysis
objects
** Bug fixes **
* metareg():
- consider argument 'intercept = FALSE' if argument 'formula' has
been provided
** Internal changes **
* New internal function replaceNULL()
*** meta, version 4.9-1, 2018-03-21 ***
** Major changes **
* Subgroup results consider the exclusion of individual studies
(bug fix)
* For generalized linear mixed models, between-study variance set to
NA if only a single study is considered in meta-analysis
** Bug fixes **
* metamean():
- use of argument 'byvar' for subgroup analyses possible
* metacor(), metamean(), metaprop(), and metarate():
- use as input to metabind() possible
* Internal function subgroup():
- consider argument 'exclude' in subgroup analyses
* Internal function bylevs():
- drop unused levels if subgroup variable is a factor variable
** User-visible changes **
* print.summary.meta():
- print information on Generalized Linear Mixed Model (GLMM) for
metarate() objects
- print information on increments added to calculate confidence
intervals for individual studies (for metarate() with GLMM)
* funnel.meta():
- new arguments 'ref.triangle', 'lty.ref', 'lwd.ref', 'col.ref',
and 'lty.ref.triangle' to add reference value (null effect) and
corresponding confidence intervals to the funnel plot
* metabin():
- new argument 'pscale' to change printout of risk differences
* metainc():
- new arguments 'irscale' and 'irunit' to change printout of
incidence rate differences
* forest.meta(), print.meta(), print.summary.meta(), update.meta():
- consider arguments 'pscale', 'irscale', and 'irunit' for
meta-analysis objects created with metabin() and metainc()
* print.meta():
- new argument 'irunit'
** Internal changes **
* metaprop():
- for random effects model, rma.glmm() from package metafor is
called internally with argument 'method = "FE"' if only a single
study is available
* metareg():
- for generalised linear mixed models, fallback to fixed effect
model if number of studies is too small for random effects
meta-regression
* asin2ir():
- back-transformation could result in (very small) negative zero
values due to imprecisions (-1e-19); these values are set to
zero now
* subgroup():
- code for metamean() added
* chkchar():
- new argument 'nchar' to test the length of character string(s)
* New internal function is.untransformed() to check for effect
measures without (back-)transformation
*** meta, version 4.9-0, 2017-12-06 ***
** Major changes **
* New function metamean() to conduct meta-analysis of single means
* New function metabind() to combine meta-analysis objects, e.g. to
generate a forest plot with results of several subgroup analyses
* Subgroup analyses implemented for generalised linear mixed models
(GLMMs) with and without assumption of common between-study
variance (arguments 'byvar' and 'tau.common')
* Axis direction can be reversed for x-axis in forest plots
* Source code version of meta can be installed without compilation,
i.e., without use of Rtools on Windows or 'Command-line tools for
Xcode' on macOS
* Rank test for funnel plot asymmetry uses cor() from R package
stats instead of internal C routine (negligibly slower, however,
no need for compilation of source installs)
* Thousands separator can be used in printouts and forest plots for
large numbers
* P-values equal to 0 are actually printed as "0" instead of
"< 0.0001"
** User-visible changes **
* forest.meta(), print.meta(), print.summary.meta():
- new argument 'big.mark' to specify character printed as
thousands separator, e.g., big.mark = "," will result in
printing of 1,000 for the number 1000
* forest.meta():
- sensible forest plot generated if first value in argument 'xlim'
is larger than second value, e.g. xlim = c(10, -10)
- separator between label and levels of grouping variable
(argument 'byseparator') is considered from meta-analysis object
- for relative summary measures, e.g., odds ratio and risk ratio,
labels on x-axis are not rounded to two digits (which resulted
in the value 0 for a tick-mark at 0.001)
- bug fix:
lines for treatment effect in fixed effect and random effects
model start in center of diamond if argument hetstat = FALSE
- bug fix:
argument 'type.study' will be sorted according to arguments 'sortvar'
* metaprop():
- arguments 'byvar' and 'tau.common' can be used for GLMMs
* Help page with overview of R functions in R package meta updated
** Internal changes **
* New internal functions:
- is.log.effect() to check for treatment effects combined on log
scale
- is.mean() to check whether summary measure refers to
meta-analysis of single means
* Renamed internal functions:
- formatCI() instead of p.ci()
- formatN() instead of format.NA()
- formatPT() instead of format.p()
* Removed R functions:
- format.tau() as functionality is now provided by formatPT()
- C program kenscore.c as cor() from R package stats is used
instead to calculate Kendall's tau
* Deprecated functions: format.NA(), format.p(), and p.ci()
* Check whether argument 'sm' is NULL in meta-analysis functions
* subgroup(): extended for GLMMs
* formatPT():
- zero p-values are printed as "0" instead of "< 0.001"
- NaNs are handled like NAs
* bylabel(), catmeth(), formatPT(), formatN(), xlab():
- new argument 'big.mark' (see above)
*** meta, version 4.8-4, 2017-08-11 ***
** User-visible changes **
* forest.meta():
- new arguments 'col.fixed' and 'col.random' to change colour of
fixed effect and random effects lines
** Bug fixes **
* bubble.metareg():
- works if covariate in metareg() is not part of dataset used to
generate meta analysis object
* forest.meta():
- lines for treatment effect in fixed effect and random effects
model always start in center of diamond
* metacum(), metainf():
- argument 'model.glmm' considered for metabin() and metainc()
objects
* print.summary.meta():
- print transformed null effect for meta-analysis of single
correlations, proportions, or rates if argument backtransf is
FALSE, i.e., for metacor(), metaprop(), and metarate() objects
* trimfill.meta():
- argument 'null.effect' is considered to calculate p-value for
fixed effect and random effects model for metacor(), metaprop(),
and metarate() objects
** Internal changes **
* New internal functions is.cor(), is.prop(), and is.rate() to check
whether summary measure refers to meta-analysis of correlations,
proportions, or rates
* metabias.default(), radial.default(), and trimfill.default():
- call metagen() internally to create meta-analysis object
- call metabias.meta(), radial.meta(), or trimfill.meta()
internally to conduct analysis
*** meta, version 4.8-3, 2017-07-21 ***
** Major changes **
* Similar to RevMan 5, individual studies can be excluded from
meta-analysis, however, will be shown in printouts and forest
plots
* In forest plots, line spacing can be determined by the user.
** User-visible changes **
* metabin(), metacor(), metacont(), metagen(), metainc(),
metaprop(), metarate():
- new argument 'exclude' to exclude studies from meta-analysis
* forest.meta():
- new argument 'spacing' to determine line spacing
- bug fix for for meta-analysis with standardized mean difference
(sm = "SMD") and argument layout = "RevMan5"
* R function ci() can be used with vectors or matrices of treatment
estimates and standard errors and a single value for argument
'df', i.e., degrees of freedom
(which is used in R package netmeta to calculate prediction
intervals for network meta-analysis estimates)
* metacum() and metainf():
- argument 'null.effect' considered internally for objects
generated with metacor(), metagen(), metaprop(), and metarate()
** Internal changes **
* baujat.meta(), metabias.meta(), metacum(), metainf(),
forest.meta(), funnel.meta(), metareg(), print.meta(),
radial.meta(), trimfill.meta(), update.meta():
- changes to deal with excluded studies
*** meta, version 4.8-2, 2017-05-24 ***
** Major changes **
* Calculate confidence interval for I-squared in a meta-analysis
with two studies if the heterogeneity statistic Q is larger than 2
* P-values can be printed in scientific notation
* In forest plots, printing of z-values can be disabled and labels
for tests can be changed by user
** User-visible changes **
* forest.meta():
- new argument 'print.zval' to print (default) or not print
z-value for test of treatment effect
- new argument 'print.Q.subgroup' to print (default) or not print
Chi-squared statistic for test of subgroup differences
- bug fix: print first line above second line if argument 'xlab'
consists of two lines (bug was introduced in meta, version
4.8-0)
- labels of additional columns are printed in correct line if
label consists of two lines
- new argument 'scientific.pval' to print p-values in scientific
notation, e.g., 1.2345e-01 instead of 0.12345
- arguments 'label.test.overall.fixed', 'label.test.overall.random',
'label.test.subgroup.fixed', 'label.test.subgroup.random',
'label.test.effect.subgroup.fixed', 'label.test.effect.subgroup.random'
work as expected
- new argument 'text.subgroup.nohet' to enable the user to change
the text "not applicable" in the line with heterogeneity
statistics for a subgroup with less than two studies
contributing to the meta-analysis
- forest plot without any study contributing to meta-analysis can
be generated without an error, e.g., meta-analysis with binary
outcome, sm="OR", and all event numbers equal to zero
* print.meta() and print.summary.meta():
- new argument 'scientific.pval' to print p-values in scientific
notation, e.g., 1.2345e-01 instead of 0.12345.
- new arguments 'print.pval' and 'print.pval.Q' to specify number
of significant digits for p-values
* R command 'help(meta)' can be used to show brief overview of R
package meta
* Substantially decrease number of automatically run examples for
forest.meta() as CRAN only allows a run time below 10 seconds for
examples provided on a help page
** Internal changes **
* new internal function pvalQ() to calculate p-value from
heterogeneity tests
* calcH():
- Calculate confidence interval for H in a meta-analysis with two
studies if the heterogeneity statistic Q is larger than 2 (this
confidence interval is used in isquared() to calculate a
confidence interval for I-squared)
* hetcalc():
- heterogeneity statistic Q set to 0 for a single study
contributing to the meta-analysis
(sometimes in this case Q was set to a value below 1e-30)
* subgroup():
- list element df.Q.b set to 0 if number of studies in
meta-analysis is 0
* format.p():
- new argument 'lab.NA' to change value printed for NAs
* forest.meta() and print.summary.meta():
- use internal function pvalQ() instead of dedicated R code
*** meta, version 4.8-1, 2017-03-17 ***
** User-visible changes **
* metacum(), metainf():
- bug fix for meta-analysis objects without continuity correction,
i.e., metacont(), metacor(), metagen() (bug was introduced in
version 4.8-0 of meta)
Error message: "Error in rep_len(x$incr, k.all): cannot
replicate NULL to a non-zero length"
- bug fix for metarate() objects (improper use of metaprop()
internally)
*** meta, version 4.8-0, 2017-03-12 ***
** Major changes **
* Continuity correction can be specified for each individual study
in meta-analysis with proportions or incidence rates
** User-visible changes **
* metabin(), metainc(), metaprop(), metarate():
- argument 'incr' can be of same length as number of studies in
meta-analysis
* metaprop():
- bug fix in studies with missing information for events or
sample size and argument method.ci = "CP"
- bug fix such that test for an overall effect is actually
calculated
* forest.meta():
- bug fix such that summary label (argument 'smlab') is printed
above forest plot if argument 'fontsize' is unequal to 12
- by default, label on x-axis and text on top of forest plot are
printed in center of forest plot (arguments 'xlab.pos',
'smlab.pos')
* print.summary.meta():
- print number of studies for fixed effect meta-analysis using
Mantel-Haenszel method if different from number of studies in
random effects model (only if summary measure is "RD" or "IRD"
and at least one study has zero events)
* metainc():
- bug fix such that argument 'incr' is considered for incidence
rate difference (sm = "IRD")
** Internal changes **
* act on NOTE in 'R CMD check ... --as-cran' with R version, 3.4.0,
i.e. register and declare native C routine kenscore
* metabin(), metainc():
- new list element 'k.MH' with number of studies in meta-analysis
using Mantel-Haenszel method
* forest.meta():
- auxiliary R functions removed from R code
- cleaning / shortening of R code
* new auxiliary R functions used in forest.meta():
- add.label, add.text, add.xlab, draw.axis, draw.ci.square,
draw.ci.diamond, draw.ci.predict, draw.forest, draw.lines,
formatcol, removeNULL, tg, tgl, twolines, wcalc
* hetcalc(), calcH():
- set tau^2 as well as H and I^2 to NA if only a single study
contributes to meta-analysis (e.g., if other studies in
meta-analysis have zero standard error)
* updateversion():
- use R function update.meta() if version of meta used to create R
object is below 3.2
*** meta, version 4.7-1, 2017-02-13 ***
** Major changes **
* Null hypothesis for test of an overall effect can be specified for
metacor(), metagen(), metaprop(), and metarate(); for all other
meta-analysis functions implicit a null effect of zero is assumed
(for relative effect measures, e.g., odds ratio and hazard ratio,
the null effect is defined on the log scale)
* User can choose whether to print the following heterogeneity
quantities: I^2, H, R_b (by default, heterogeneity measure R_b is
not printed and thus revoking a change in meta, 4.7-0)
* In forest plots with subgroups, study weights are summed up to 100
percent within each subgroup if no overall estimates are
requested, i.e., argument overall is FALSE (like before, by
default, weights are not printed if argument overall is FALSE and
have to be explicitely requested using argument leftcols or
rightcols)
** User-visible changes **
* forest.meta():
- print line with heterogeneity statistics directly below
individual study results if pooled effects are not shown
in forest plot (overall = FALSE)
- print right and left labels (arguments label.left, label.right)
in correct line if arguments overall and addrow are FALSE
- bug fix: do not stop with an error if comb.fixed = FALSE,
comb.random = FALSE, and overall.hetstat = TRUE
* ci(), metacor(), metagen(), metaprop(), metarate():
- new argument null.effect to specify null hypothesis for test of
an overall effect, e.g., null.effect = 0.5 in metaprop() to test
whether the overall proportion is equal to 0.5
* metagen():
- Hartung-Knapp method only used for at least two studies in
meta-analysis
* print.meta():
- print covariate with subgroup information for each study, if
subgroup analysis is conducted (argument byvar)
* print.summary.meta():
- new arguments print.I2, print.H, print.Rb to specify
heterogeneity measures shown in output
- new arguments text.tau2, text.I2, text.Rb to change text printed
to identify respective heterogeneity measure
- only print information on double zero studies if argument
allstudies is TRUE
- print results for (empty) subgroup in meta-analysis with two
studies and one subgroup with missing treatment estimate
* settings.meta():
- new arguments print.I2, print.H, print.Rb, text.tau2, text.I2,
text.Rb to modify printing of heterogeneity measures
** Internal changes **
* summary.meta():
- bug fix: list element 'ircale' renamed to 'irscale'
- list element 'within' removed which has not been used since
meta, version 1.1-4
*** 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:
- R_b (Crippa et al., 2016, <DOI:10.1002/sim.6980>)
* 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
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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)
*** meta, 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.
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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
*** 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.
*** meta, 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.
*** meta, 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)
*** 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
*** meta, 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)
*** 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"
*** meta, 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)
*** meta, 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.
*** meta, 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)
*** 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.
*** meta, 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 in version 2.4-0 of
meta)
- 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
*** meta, 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)
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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]) ...'
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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"
*** meta, 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
*** meta, 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.
*** meta, 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
*** meta, 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
*** 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.
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 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
*** meta, 2009-10-30, version 1.1-3 ***
New functions trimfill, trimfill.default and trimfill.meta:
- generic method for trim-and-fill method
*** meta, 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
*** meta, 2009-08-31, version 1.0-6 ***
** First major version released on CRAN **
Note, no NEWS available for versions < 1.0
*** meta, 2009-04-09, version 0.9-19 ***
*** meta, 2009-03-03, version 0.9-18 ***
*** meta, 2009-01-28, version 0.9-17 ***
*** meta, 2008-12-08, version 0.9-15 ***
*** meta, 2007-02-13, version 0.8-2 ***
*** meta, 2006-11-29, version 0.81 ***
*** meta, 2006-11-24, version 0.8 ***
*** meta, 2005-02-23, version 0.5-0 ***
** First version released on CRAN (2006-02-08) **
