The metafor Package

A Meta-Analysis Package for R

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updates_old [2019/05/25 14:46]
Wolfgang Viechtbauer
updates_old [2019/05/25 18:07] (current)
Wolfgang Viechtbauer
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 Older updates of the metafor package are archived on this page. More recent updates can be found [[updates|here]]. Older updates of the metafor package are archived on this page. More recent updates can be found [[updates|here]].
  
-==== Changes in Version 1.9-7 (2015-05-22) ====+==== Version 1.9-7 (2015-05-22) ====
  
   * default optimizer for ''​rma.mv()''​ changed to ''​nlminb()''​ (instead of ''​optim()''​ with ''"​Nelder-Mead"''​);​ extensive testing indicated that ''​nlminb()''​ (and also ''​optim()''​ with ''"​BFGS"''​) is typically quicker and more robust; note that this is in principle a non-backwards compatible change, but really a necessary one; and you can always revert to the old behavior with ''​control=list(optimizer="​optim",​ optmethod="​Nelder-Mead"​)''​   * default optimizer for ''​rma.mv()''​ changed to ''​nlminb()''​ (instead of ''​optim()''​ with ''"​Nelder-Mead"''​);​ extensive testing indicated that ''​nlminb()''​ (and also ''​optim()''​ with ''"​BFGS"''​) is typically quicker and more robust; note that this is in principle a non-backwards compatible change, but really a necessary one; and you can always revert to the old behavior with ''​control=list(optimizer="​optim",​ optmethod="​Nelder-Mead"​)''​
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   * changed a few ''​is_identical_to()''​ comparisons to ''​expect_equivalent()''​ ones (that failed on Sparc Solaris)   * changed a few ''​is_identical_to()''​ comparisons to ''​expect_equivalent()''​ ones (that failed on Sparc Solaris)
  
-==== Changes in Version 1.9-6 (2015-05-07) ====+==== Version 1.9-6 (2015-05-07) ====
  
   * ''​funnel()''​ now works again for ''​rma.glmm''​ objects (note to self: quit breaking things that work!)   * ''​funnel()''​ now works again for ''​rma.glmm''​ objects (note to self: quit breaking things that work!)
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   * metafor now depends on at least version 3.1.0 of R   * metafor now depends on at least version 3.1.0 of R
  
-==== Changes in Version 1.9-5 (2014-11-24) ====+==== Version 1.9-5 (2014-11-24) ====
  
   * moved the ''​stats''​ and ''​Matrix''​ packages from ''​Depends''​ to ''​Imports'';​ as a result, had to add ''​utils''​ to ''​Imports'';​ moved the ''​Formula''​ package from ''​Depends''​ to ''​Suggests''​   * moved the ''​stats''​ and ''​Matrix''​ packages from ''​Depends''​ to ''​Imports'';​ as a result, had to add ''​utils''​ to ''​Imports'';​ moved the ''​Formula''​ package from ''​Depends''​ to ''​Suggests''​
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   * oh, and guess what? I updated the documentation ...   * oh, and guess what? I updated the documentation ...
  
-==== Changes in Version 1.9-4 (2014-07-30) ====+==== Version 1.9-4 (2014-07-30) ====
  
   * added ''​method="​GENQ"''​ to ''​rma.uni()''​ for the generalized Q-statistic estimator of tau^2, which allows for used-defined weights (note: the DL and HE estimators are just special cases of this method)   * added ''​method="​GENQ"''​ to ''​rma.uni()''​ for the generalized Q-statistic estimator of tau^2, which allows for used-defined weights (note: the DL and HE estimators are just special cases of this method)
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   * some improvements to the documentation (do I still need to mention this every time?)   * some improvements to the documentation (do I still need to mention this every time?)
  
-==== Changes in Version 1.9-3 (2014-05-05) ====+==== Version 1.9-3 (2014-05-05) ====
  
   * some minor tweaks to ''​rma.uni()''​ that should be user transparent   * some minor tweaks to ''​rma.uni()''​ that should be user transparent
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   * guess what? some improvements to the documentation! (also combined some of the help files to reduce the size of the manual a bit; and yes, it's still way too big)   * guess what? some improvements to the documentation! (also combined some of the help files to reduce the size of the manual a bit; and yes, it's still way too big)
  
-==== Changes in Version 1.9-2 (2013-10-07) ====+==== Version 1.9-2 (2013-10-07) ====
  
   * added function ''​rma.mv()''​ to fit multivariate/​multilevel meta-analytic models via appropriate linear (mixed-effects) models; this function allows for modeling of non-independent sampling errors and/or true effects and can be used for network meta-analyses,​ meta-analyses accounting for phylogenetic relatedness,​ and other complicated meta-analytic data structures   * added function ''​rma.mv()''​ to fit multivariate/​multilevel meta-analytic models via appropriate linear (mixed-effects) models; this function allows for modeling of non-independent sampling errors and/or true effects and can be used for network meta-analyses,​ meta-analyses accounting for phylogenetic relatedness,​ and other complicated meta-analytic data structures
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   * some improvements to the documentation (as always)   * some improvements to the documentation (as always)
  
-==== Changes in Version 1.9-1 (2013-07-20) ====+==== Version 1.9-1 (2013-07-20) ====
  
   * ''​rma.mh()''​ now also implements the Mantel-Haenszel method for incidence rate differences (''​measure="​IRD"''​)   * ''​rma.mh()''​ now also implements the Mantel-Haenszel method for incidence rate differences (''​measure="​IRD"''​)
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   * some improvements to the documentation   * some improvements to the documentation
  
-==== Changes in Version 1.9-0 (2013-06-21) ====+==== Version 1.9-0 (2013-06-21) ====
  
   * vignette renamed to '​metafor'​ so ''​vignette("​metafor"​)''​ works now   * vignette renamed to '​metafor'​ so ''​vignette("​metafor"​)''​ works now
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   * some improvements to the documentation   * some improvements to the documentation
  
-==== Changes in Version 1.8-0 (2013-04-11) ====+==== Version 1.8-0 (2013-04-11) ====
  
   * added additional clarifications about the change score outcome measures (''"​MC"'',​ ''"​SMCC"'',​ and ''"​SMCR"''​) to the help file for the ''​escalc()''​ function and changed the code so that ''"​SMCR"''​ no longer expects argument ''​sd2i''​ to be specified (which is not needed anyways) (thanks to Markus Kösters for bringing this to my attention)   * added additional clarifications about the change score outcome measures (''"​MC"'',​ ''"​SMCC"'',​ and ''"​SMCR"''​) to the help file for the ''​escalc()''​ function and changed the code so that ''"​SMCR"''​ no longer expects argument ''​sd2i''​ to be specified (which is not needed anyways) (thanks to Markus Kösters for bringing this to my attention)
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   * some improvements to the documentation   * some improvements to the documentation
  
-==== Changes in Version 1.7-0 (2013-02-06) ====+==== Version 1.7-0 (2013-02-06) ====
  
   * added ''​rma.glmm()''​ function for fitting of appropriate generalized linear (mixed-effects) models when analyzing odds ratios, incidence rate ratios, proportions,​ or rates; the function makes use of the ''​lme4''​ and ''​BiasedUrn''​ packages; these are now suggested packages and loaded within ''​rma.glmm()''​ only when required (this makes for faster loading of the ''​metafor''​ package)   * added ''​rma.glmm()''​ function for fitting of appropriate generalized linear (mixed-effects) models when analyzing odds ratios, incidence rate ratios, proportions,​ or rates; the function makes use of the ''​lme4''​ and ''​BiasedUrn''​ packages; these are now suggested packages and loaded within ''​rma.glmm()''​ only when required (this makes for faster loading of the ''​metafor''​ package)
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   * some improvements to the documentation   * some improvements to the documentation
  
-==== Changes in Version 1.6-0 (2011-04-13) ====+==== Version 1.6-0 (2011-04-13) ====
  
   * ''​trimfill.rma()''​ now returns a proper object even when the number of missing studies is estimated to be zero   * ''​trimfill.rma()''​ now returns a proper object even when the number of missing studies is estimated to be zero
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   * some improvements to the documentation   * some improvements to the documentation
  
-==== Changes in Version 1.5-0 (2010-12-16) ====+==== Version 1.5-0 (2010-12-16) ====
  
   * added ''​labbe()''​ function to create L’Abbe plots   * added ''​labbe()''​ function to create L’Abbe plots
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   * some improvements to the documentation   * some improvements to the documentation
  
-==== Changes in Version 1.4-0 (2010-07-30) ====+==== Version 1.4-0 (2010-07-30) ====
  
   * the package has now been published in the Journal of Statistical Software ([[http://​www.jstatsoft.org/​v36/​i03/​]])   * the package has now been published in the Journal of Statistical Software ([[http://​www.jstatsoft.org/​v36/​i03/​]])
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   * some updates to the documentation   * some updates to the documentation
  
-==== Changes in Version 1.3-0 (2010-06-25) ====+==== Version 1.3-0 (2010-06-25) ====
  
   * metafor package now depends on Formula package   * metafor package now depends on Formula package
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   * added the (inverse) arcsine transformation to the set of transformation functions   * added the (inverse) arcsine transformation to the set of transformation functions
  
-==== Changes in Version 1.2-0 (2010-05-18) ====+==== Version 1.2-0 (2010-05-18) ====
  
   * cases where k is very small (e.g., k equal to 1 or 2) are now handled more gracefully   * cases where k is very small (e.g., k equal to 1 or 2) are now handled more gracefully
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   * ''​logLik.rma()''​ function now behaves more like other ''​logLik()''​ functions (such as ''​logLik.lm()''​ and ''​logLik.lme()''​)   * ''​logLik.rma()''​ function now behaves more like other ''​logLik()''​ functions (such as ''​logLik.lm()''​ and ''​logLik.lme()''​)
  
-==== Changes in Version 1.1-0 (2010-04-28) ====+==== Version 1.1-0 (2010-04-28) ====
  
   * ''​cint()''​ generic removed and replaced with ''​confint()''​ method for ''​rma.uni''​ objects   * ''​cint()''​ generic removed and replaced with ''​confint()''​ method for ''​rma.uni''​ objects
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   * changed the default number of iterations for the ML, REML, and EB estimators from 50 to 100   * changed the default number of iterations for the ML, REML, and EB estimators from 50 to 100
  
-==== Changes in Version 1.0-1 (2010-02-02) ====+==== Version 1.0-1 (2010-02-02) ====
  
   * version jump in conjunction with the upcoming publication of a paper in the Journal of Statistical Software describing the package   * version jump in conjunction with the upcoming publication of a paper in the Journal of Statistical Software describing the package
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   * some small improvements to the documentation   * some small improvements to the documentation
  
-==== Changes in Version 0.5-7 (2009-12-06) ====+==== Version 0.5-7 (2009-12-06) ====
  
   * added ''​permutest()''​ function for permutation tests   * added ''​permutest()''​ function for permutation tests
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   * a bit of code reorganization (nothing that affects how the functions work)   * a bit of code reorganization (nothing that affects how the functions work)
  
-==== Changes in Version 0.5-6 (2009-10-19) ====+==== Version 0.5-6 (2009-10-19) ====
  
   * small changes to the computation of the DFFITS and DFBETAS values in the ''​influence()''​ function, so that these statistics are more in line with their definitions in regular linear regression models   * small changes to the computation of the DFFITS and DFBETAS values in the ''​influence()''​ function, so that these statistics are more in line with their definitions in regular linear regression models
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   * added a control option to ''​rma()''​ to adjust the step length of the Fisher scoring algorithm by a constant factor (this may be useful when the algorithm does not converge)   * added a control option to ''​rma()''​ to adjust the step length of the Fisher scoring algorithm by a constant factor (this may be useful when the algorithm does not converge)
  
-==== Changes in Version 0.5-5 (2009-10-08) ====+==== Version 0.5-5 (2009-10-08) ====
  
   * added the phi coefficient (''​measure="​PHI"''​),​ Yule's Q (''"​YUQ"''​),​ and Yule's Y (''"​YUY"''​) as additional measures to the ''​escalc()''​ function for 2x2 table data   * added the phi coefficient (''​measure="​PHI"''​),​ Yule's Q (''"​YUQ"''​),​ and Yule's Y (''"​YUY"''​) as additional measures to the ''​escalc()''​ function for 2x2 table data
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   * some small corrections to the documentation   * some small corrections to the documentation
  
-==== Changes in Version 0.5-4 (2009-09-18) ====+==== Version 0.5-4 (2009-09-18) ====
  
   * corrected the ''​trimfill()''​ function   * corrected the ''​trimfill()''​ function
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   * some small corrections to the documentation   * some small corrections to the documentation
  
-==== Changes in Version 0.5-3 (2009-07-31) ====+==== Version 0.5-3 (2009-07-31) ====
  
   * small changes to some of the examples   * small changes to some of the examples
   * added the log transformed proportion (''​measure="​PLN"''​) as another measure to the ''​escalc()''​ function; changed ''"​PL"''​ to ''"​PLO"''​ for the logit (i.e., log odds) transformation for proportions   * added the log transformed proportion (''​measure="​PLN"''​) as another measure to the ''​escalc()''​ function; changed ''"​PL"''​ to ''"​PLO"''​ for the logit (i.e., log odds) transformation for proportions
  
-==== Changes in Version 0.5-2 (2009-07-06) ====+==== Version 0.5-2 (2009-07-06) ====
  
   * added an option in ''​plot.infl.rma.uni()''​ to open a new device for plotting the DFBETAS values   * added an option in ''​plot.infl.rma.uni()''​ to open a new device for plotting the DFBETAS values
   * thanks to Jim Lemon, added a much better method of adjusting the size of the labels, annotations,​ and symbols in the ''​forest()''​ function when the number of studies is large   * thanks to Jim Lemon, added a much better method of adjusting the size of the labels, annotations,​ and symbols in the ''​forest()''​ function when the number of studies is large
  
-==== Changes in Version 0.5-1 (2009-06-14) ====+==== Version 0.5-1 (2009-06-14) ====
  
   * made some small changes to the documentation (some typos corrected, some confusing points clarified)   * made some small changes to the documentation (some typos corrected, some confusing points clarified)
  
-==== Changes in Version 0.5-0 (2009-06-05) ====+==== Version 0.5-0 (2009-06-05) ====
  
   * first version released on CRAN   * first version released on CRAN
  
updates_old.txt · Last modified: 2019/05/25 18:07 by Wolfgang Viechtbauer