updates

**This is an old revision of the document!**

On this page, you can find a description of the (recent) updates to the metafor package. Older updates are archived here.

- added
`simulate()`

method for`rma`

objects; added`MASS`

to`Suggests`

(since simulating for`rma.mv`

objects requires`mvrnorm()`

from`MASS`

) `cooks.distance.rma.mv()`

now works properly even when there are missing values in the data`residuals()`

gains`type`

argument and can compute Pearson residuals- the
`newmods`

argument in`predict()`

can now be a named vector or a matrix/data frame with column names that get properly matched up with the variables in the model - added
`ranef.rma.mv()`

for extracting the BLUPs of the random effects for`rma.mv`

models - all functions that repeatedly refit models now have the option to show a progress bar
- added
`ranktest.default()`

, so user can now pass the outcomes and corresponding sampling variances directly to the function - added
`regtest.default()`

, so user can now pass the outcomes and corresponding sampling variances directly to the function `funnel.default()`

gains`subset`

argument`funnel.default()`

and`funnel.rma()`

gain`col`

and`bg`

arguments`plot.profile.rma()`

gains`ylab`

argument- more consistent handling of
`robust.rma`

objects - added location-scale model
- added a print method for
`rma.gosh`

objects - the (log) relative risk is now called the (log) risk ratio in all help files, plots, code, and comments
`escalc()`

can now compute outcome measures based on paired binary data (`"MPRR"`

,`"MPOR"`

,`"MPRD"`

,`"MPORC"`

, and`"MPPETO"`

)`escalc()`

can now compute (semi-)partial correlation coefficients (`"PCOR"`

,`"ZPCOR"`

,`"SPCOR"`

)`escalc()`

can now compute measures of variability for single groups (`"CVLN"`

,`"SDLN"`

) and for the difference in variability between two groups (`"CVR"`

,`"VR"`

); also the log transformed mean (`"MNLN"`

) has been added for consistency`escalc()`

can now compute the sampling variance for`measure="PHI"`

for studies using stratified sampling (`vtpye="ST"`

)- the
``[``

method for`escalc`

objects now properly handles the`ni`

and`slab`

attributes and does a better job of cleaning out superfluous variable name information - added
`rbind()`

method for`escalc`

objects - added
`as.data.frame()`

method for`list.rma`

objects - added a new dataset (
`dat.pagliaro1992`

) for another illustration of a network meta-analysis - added a new dataset (
`dat.laopaiboon2015`

) on the effectiveness of azithromycin for treating lower respiratory tract infections `rma.uni()`

and`rma.mv()`

now check if the ratio of the largest to smallest sampling variance is very large; results may not be stable then (and very large ratios typically indicate wrongly coded data)- model fitting functions now check if extra/superfluous arguments are specified via
`...`

and issues are warning if so - instead of defining own generic
`ranef()`

, import`ranef()`

from`nlme`

- improved output formatting
- added more tests (but disabled a few tests on CRAN to avoid some issues when R is compiled with
`--disable-long-double`

) - some general code cleanup
- renamed diagram_metafor.pdf vignette to just diagram.pdf
- minor updates in the documentation

- started to use git as version control system, GitHub to host the repository (https://github.com/wviechtb/metafor) for the development version of the package, Travis CI as continuous integration service (https://travis-ci.org/wviechtb/metafor), and Codecov for automated code coverage reporting (https://codecov.io/github/wviechtb/metafor)
- argument
`knha`

in`rma.uni()`

and argument`tdist`

in`rma.glmm()`

and`rma.mv()`

are now superseded by argument`test`

in all three functions; for backwards compatibility, the`knha`

and`tdist`

arguments still work, but are no longer documented `rma(yi, vi, weights=1, test="knha")`

now yields the same results as`rma(yi, vi, weighted=FALSE, test="knha")`

(but use of the Knapp and Hartung method in the context of an unweighted analysis remains an experimental feature)- one can now pass an
`escalc`

object directly to`rma.uni()`

, which then tries to automatically determine the`yi`

and`vi`

variables in the data frame (thanks to Christian Röver for the suggestion) `escalc()`

can now also be used to convert a regular data frame to an`escalc`

object- for
`measure="UCOR"`

, the exact bias-correction is now used (instead of the approximation); when`vtype="UB"`

, the exact equation is now used to compute the unbiased estimate of the variance of the bias-corrected correlation coefficient; hence`gsl`

is now a suggested package (needed to compute the hypergeometric function) and is loaded when required `cooks.distance()`

now also works with`rma.mv`

objects; and since model fitting can take some time, an option to show a progress bar has been added- fixed an issue with
`robust.rma.mv()`

throwing errors when the model was fitted with`sparse=TRUE`

- fixed an error with
`robust.rma.mv()`

when the model was fitted with user-defined weights (or a user-defined weight matrix) - added
`ranef()`

for extracting the BLUPs of the random effects (only for`rma.uni`

objects at the moment) - reverted back to the pre-1.1-0 way of computing p-values for individual coefficients in
`permutest.rma.uni()`

, that is, the p-value is computed with`mean(abs(z_perm) >= abs(z_obs) - tol)`

(where`tol`

is a numerical tolerance) `permutest.rma.uni()`

gains`permci`

argument, which can be used to obtain permutation-based CIs of the model coefficients (note that this is computationally very demanding and may take a long time to complete)`rma.glmm()`

continues to work even when the saturated model cannot be fitted (although the tests for heterogeneity are not available then)`rma.glmm()`

now allows control over the arguments used for`method.args`

(via`control=list(hessianCtrl=list(...))`

) passed to`hessian()`

(from the`numDeriv`

package) when using`model="CM.EL"`

and`measure="OR"`

- in
`rma.glmm()`

, default`method.args`

value for`r`

passed to`hessian()`

has been increased to 16 (while this slows things down a bit, this appears to improve the accuracy of the numerical approximation to the Hessian, especially when tau^2 is close to 0) - the various
`forest()`

and`addpoly()`

functions now have a new argument called`width`

, which provides manual control over the width of the annotation columns; this is useful when creating complex forest plots with a monospaced font and we want to ensure that all annotations are properly lined up at the decimal point - the annotations created by the various
`forest()`

and`addpoly()`

functions are now a bit more compact by default - more flexible
`efac`

argument in the various`forest()`

functions - trailing zeros in the axis labels are now dropped in forest and funnel plots by default; but trailing zeros can be retained by specifying a numeric (and not an integer) value for the
`digits`

argument - added
`funnel.default()`

, which directly takes as input a vector with the observed effect sizes or outcomes and the corresponding sampling variances, standard errors, and/or sample sizes - added
`plot.profile.rma()`

, a plot method for objects returned by the`profile.rma.uni()`

and`profile.rma.mv()`

functions - simplified
`baujat.rma.uni()`

,`baujat.rma.mh()`

, and`baujat.rma.peto()`

to`baujat.rma()`

, which now handles objects of class`rma.uni`

,`rma.mh`

, and`rma.peto`

`baujat.rma()`

gains argument`symbol`

for more control over the plotting symbol`labbe()`

gains a`grid`

argument- more logical placement of labels in
`qqnorm.rma.uni()`

,`qqnorm.rma.mh()`

, and`qqnorm.rma.peto()`

functions (and more control thereof) `qqnorm.rma.uni()`

gains`lty`

argument- added
`gosh.rma()`

and`plot.gosh.rma()`

for creating GOSH (i.e., graphical display of study heterogeneity) plots based on Olkin et al. (2012) - in the (rare) case where all observed outcomes are exactly equal to each other,
`test="knha"`

(i.e.,`knha=TRUE`

) in`rma()`

now leads to more appropriate results - updated datasets so those containing precomputed effect size estimates or observed outcomes are already declared to be
`escalc`

objects - added new datasets (
`dat.egger2001`

and`dat.li2007`

) on the effectiveness of intravenous magnesium in acute myocardial infarction `methods`

package is now under`Depends`

(in addition to`Matrix`

), so that`rma.mv(..., sparse=TRUE)`

always works, even under Rscript- some general code cleanup
- added more tests (and used a more consistent naming scheme for tests)

- due to more stringent package testing, it is increasingly difficult to ensure that the package passes all checks on older versions of R; from now on, the package will therefore require, and be checked under, only the current (and the development) version of R
- added
`graphics`

,`grDevices`

, and`methods`

to Imports (due to recent change in how CRAN checks packages) - the
`struct`

argument for`rma.mv()`

now also allows for`"ID"`

and`"DIAG"`

, which are identical to the`"CS"`

and`"HCS"`

structures, but with the correlation parameter fixed to 0 - added
`robust()`

for (cluster) robust tests and confidence intervals for`rma.uni`

and`rma.mv`

models (this uses a robust sandwich-type estimator of the variance-covariance matrix of the fixed effects along the lines of the Eicker-Huber-White method) `confint()`

now works for models fitted with the`rma.mv()`

function; for variance and correlation parameters, the function provides profile likelihood confidence intervals; the output generated by the`confint()`

function has been adjusted in general to make the formatting more consistent across the different model types- for objects of class
`rma.mv`

,`profile()`

now provides profile plots for all (non-fixed) variance and correlation components of the model when no component is specified by the user (via the`sigma2`

,`tau2`

,`rho`

,`gamma2`

, or`phi`

arguments) - for
`measure="MD"`

and`measure="ROM"`

, one can now choose between`vtype="LS"`

(the default) and`vtype="HO"`

; the former computes the sampling variances without assuming homoscedasticity, while the latter assumes homoscedasticity - multiple model objects can now be passed to the
`fitstats()`

,`AIC()`

, and`BIC()`

functions - check for duplicates in the
`slab`

argument is now done *after* any subsetting is done (as suggested by Michael Dewey) `rma.glmm()`

now again works when using`add=0`

, in which case some of the observed outcomes (e.g., log odds or log odds ratios) may be`NA`

- when using
`rma.glmm()`

with`model="CM.EL"`

, the saturated model (used to compute the Wald-type and likelihood ratio tests for the presence of (residual) heterogeneity) often fails to converge; the function now continues to run (instead of stopping with an error) and simply omits the test results from the output - when using
`rma.glmm()`

with`model="CM.EL"`

and inversion of the Hessian fails via the Choleski factorization, the function now makes another attempt via the QR decomposition (even when this works, a warning is issued) - for
`rma.glmm()`

, BIC and AICc values were switched around; corrected - more use of
`suppressWarnings()`

is made when functions repeatedly need to fit the same model, such as`cumul()`

,`influence()`

, and`profile()`

; that way, one does not get inundated with the same warning(s) - some (overdue) updates to the documentation

- 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")`

- all tests have been updated in accordance with the recommended syntax of the
`testthat`

package; for example,`expect_equivalent(x,y)`

is used instead of`test_that(x, is_equivalent_to(y))`

- changed a few
`is_identical_to()`

comparisons to`expect_equivalent()`

ones (that failed on Sparc Solaris)

`funnel()`

now works again for`rma.glmm`

objects (note to self: quit breaking things that work!)`rma.glmm()`

will now only issue a warning (and not an error) when the Hessian for the saturated model cannot be inverted (which is needed to compute the Wald-type test for heterogeneity, so the test statistic is then simply set to`NA`

)`rma.mv()`

now allows for two terms of the form`~ inner | outer`

; the variance components corresponding to such a structure are called`gamma2`

and correlations are called`phi`

; other functions that work with objects of class`rma.mv`

have been updated accordingly`rma.mv()`

now provides (even) more optimizer choices:`nlm()`

from the`stats`

package,`hjk()`

and`nmk()`

from the`dfoptim`

package, and`ucminf()`

from the`ucminf`

package; choose the desired optimizer via the`control`

argument (e.g.,`control=list(optimizer="nlm")`

)`profile.rma.uni()`

and`profile.rma.mv()`

now can do parallel processing (which is especially relevant for`rma.mv`

objects, where profiling is crucial and model fitting can be slow)- the various
`confint()`

functions now have a`transf`

argument (to apply some kind of transformation to the model coefficients and confidence interval bounds); coefficients and bounds for objects of class`rma.mh`

and`rma.peto`

are no longer automatically transformed - the various
`forest()`

functions no longer enforce that the actual x-axis limits (`alim`

) encompass the observed outcomes to be plotted; also, outcomes below or above the actual x-axis limits are no longer shown - the various
`forest()`

functions now provide control over the horizontal lines (at the top/bottom) that are automatically added to the plot via the`lty`

argument (this also allows for removing them); also, the vertical reference line is now placed *behind* the points/CIs `forest.default()`

now has argument`col`

which can be used to specify the color(s) to be used for drawing the study labels, points, CIs, and annotations- the
`efac`

argument for`forest.rma()`

now also allows two values, the first for the arrows and CI limits, the second for summary estimates - corrected some axis labels in various plots when
`measure="PLO"`

- axes in
`labbe()`

plots now have`"(Group 1)"`

and`"(Group 2)"`

added by default `anova.rma()`

gains argument`L`

for specifying linear combinations of the coefficients in the model that should be tested to be zero- in case removal of a row of data would lead to one or more inestimable model coefficients,
`baujat()`

,`cooks.distance()`

,`dfbetas()`

,`influence()`

, and`rstudent()`

could fail for`rma.uni`

objects; such cases are now handled properly - for models with moderators, the
`predict()`

function now shows the study labels when they have been specified by the user (and`newmods`

is not used) - if there is only one fixed effect (model coefficient) in the model, the
`print.infl.rma.uni()`

function now shows the DFBETAS values with the other case diagnostics in a single table (for easier inspection); if there is more than one fixed effect, a separate table is still used for the DFBETAS values (with one column for each coefficient) - added
`measure="SMCRH"`

to the`escalc()`

function for the standardized mean change using raw score standardization with heteroscedastic population variances at the two measurement occasions - added
`measure="ROMC"`

to the`escalc()`

function for the (log transformed) ratio of means (response ratio) when the means reflect two measurement occasions (e.g., for a single group of people) and hence are correlated - added own function for computing/estimating the tetrachoric correlation coefficient (for
`measure="RTET"`

); package therefore no longer suggests`polycor`

but now suggest`mvtnorm`

(which is loaded as needed) - element
`fill`

returned by`trimfill.rma.uni()`

is now a logical vector (instead of a 0/1 dummy variable) `print.list.rma()`

now also returns the printed results invisibly as a data frame- added a new dataset (
`dat.senn2013`

) as another illustration of a network meta-analysis - metafor now depends on at least version 3.1.0 of R

- 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`

- added
`update.rma()`

function (for updating/refitting a model); model objects also now store and keep the call - the
`vcov()`

function now also extracts the marginal variance-covariance matrix of the observed effect sizes or outcomes from a fitted model (of class`rma.uni`

or`rma.mv`

) `rma.mv()`

now makes use of the Cholesky decomposition when there is a`random = ~ inner | outer`

formula and`struct="UN"`

; this is numerically more stable than the old approach that avoided non-positive definite solutions by forcing the log-likelihood to be`-Inf`

in those cases; the old behavior can be restored with`control = list(cholesky=FALSE)`

`rma.mv()`

now requires the`inner`

variable in an`~ inner | outer`

formula to be a factor or character variable (except when`struct`

is`"AR"`

or`"HAR"`

); use`~ factor(inner) | outer`

in case it isn't`anova.rma.uni()`

function changed to`anova.rma()`

that works now for both`rma.uni`

and`rma.mv`

objects- the
`profile.rma.mv()`

function now omits the number of the variance or correlation component from the plot title and x-axis label when the model only includes one of the respective parameters `profile()`

functions now pass on the`...`

argument also to the`title()`

function used to create the figure titles (esp. relevant when using the`cex.main`

argument)- the
`drop00`

argument of the`rma.mh()`

and`rma.peto()`

functions now also accepts a vector with two logicals, the first applies when calculating the observed outcomes, the second when applying the Mantel-Haenszel or Peto's method `weights.rma.uni()`

now shows the correct weights when`weighted=FALSE`

- argument
`showweight`

renamed to`showweights`

in the`forest.default()`

and`forest.rma()`

functions (more consistent with the naming of the various`weights()`

functions) - added
`model.matrix.rma()`

function (to extract the model matrix from objects of class`rma`

) `funnel()`

and`radial()`

now (invisibly) return data frames with the coordinates of the points that were drawn (may be useful for manual labeling of points in the plots)`permutest.rma.uni()`

function now uses a numerical tolerance when making comparisons (>= or ⇐) between an observed test statistic and the test statistic under the permuted data; when using random permutations, the function now ensures that the very first permutation correspond to the original data- corrected some missing/redundant row/column labels in some output
- most
`require()`

calls replaced with`requireNamespace()`

to avoid altering the search path (hopefully this won't break stuff ...) - some non-visible changes including more use of some (non-exported) helper functions for common tasks
- dataset
`dat.collins91985a`

updated (including all reported outcomes and some more information about the various trials) - oh, and guess what? I updated the documentation ...

Older updates are archived here.

updates.1525539293.txt.gz · Last modified: 2018/05/05 16:54 by 127.0.0.1

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