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
(Author of R function mpaule.default is
S. Cowen 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" 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