Extract tau^2 from the model object where possible when using an inte…

…gral transformation.
wviechtb · Nov 22, 2024 · 00d51a1 · 00d51a1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metafor
-Version: 4.7-54
-Date: 2024-11-21
+Version: 4.7-55
+Date: 2024-11-22
 Title: Meta-Analysis Package for R
 Authors@R: person(given = "Wolfgang", family = "Viechtbauer", role = c("aut","cre"), email = "[email protected]", comment = c(ORCID = "0000-0003-3463-4063"))
 Depends: R (>= 4.0.0), methods, Matrix, metadat, numDeriv

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# metafor 4.7-54 (2024-11-21)
+# metafor 4.7-55 (2024-11-22)
 
 - some general changes to the various `forest()` functions: argument `header` is now `TRUE` by default, the y-axis is now created with `yaxs="i"`, and the y-axis limits have been tweaked slightly in accordance
 

diff --git a/R/confint.rma.uni.r b/R/confint.rma.uni.r
@@ -41,6 +41,11 @@ confint.rma.uni <- function(object, parm, level, fixed=FALSE, random=TRUE, type,
    if (missing(targs))
       targs <- NULL
 
+   funlist <- lapply(list(transf.exp.int, transf.ilogit.int, transf.ztor.int, transf.exp.mode, transf.ilogit.mode, transf.ztor.mode), deparse)
+
+   if (is.null(targs) && any(sapply(funlist, identical, deparse(transf))) && inherits(x, c("rma.uni","rma.glmm")) && length(x$tau2 == 1L))
+      targs <- c(tau2=x$tau2)
+
    if (missing(control))
       control <- list()
 

diff --git a/R/confint.rma.uni.selmodel.r b/R/confint.rma.uni.selmodel.r
@@ -33,6 +33,11 @@ confint.rma.uni.selmodel <- function(object, parm, level, fixed=FALSE, tau2, del
    if (missing(targs))
       targs <- NULL
 
+   funlist <- lapply(list(transf.exp.int, transf.ilogit.int, transf.ztor.int, transf.exp.mode, transf.ilogit.mode, transf.ztor.mode), deparse)
+
+   if (is.null(targs) && any(sapply(funlist, identical, deparse(transf))) && inherits(x, c("rma.uni","rma.glmm")) && length(x$tau2 == 1L))
+      targs <- c(tau2=x$tau2)
+
    if (missing(control))
       control <- list()
 

diff --git a/R/cumul.rma.uni.r b/R/cumul.rma.uni.r
@@ -27,6 +27,11 @@ cumul.rma.uni <- function(x, order, digits, transf, targs, collapse=FALSE, progb
    if (missing(targs))
       targs <- NULL
 
+   funlist <- lapply(list(transf.exp.int, transf.ilogit.int, transf.ztor.int, transf.exp.mode, transf.ilogit.mode, transf.ztor.mode), deparse)
+
+   if (is.null(targs) && any(sapply(funlist, identical, deparse(transf))) && inherits(x, c("rma.uni","rma.glmm")) && length(x$tau2 == 1L))
+      targs <- c(tau2=x$tau2)
+
    ddd <- list(...)
 
    .chkdots(ddd, c("time", "decreasing"))

diff --git a/R/hc.rma.uni.r b/R/hc.rma.uni.r
@@ -24,6 +24,11 @@ hc.rma.uni <- function(object, digits, transf, targs, control, ...) {
    if (missing(targs))
       targs <- NULL
 
+   funlist <- lapply(list(transf.exp.int, transf.ilogit.int, transf.ztor.int, transf.exp.mode, transf.ilogit.mode, transf.ztor.mode), deparse)
+
+   if (is.null(targs) && any(sapply(funlist, identical, deparse(transf))) && inherits(x, c("rma.uni","rma.glmm")) && length(x$tau2 == 1L))
+      targs <- c(tau2=x$tau2)
+
    yi <- x$yi
    vi <- x$vi
    k  <- length(yi)

diff --git a/R/leave1out.rma.uni.r b/R/leave1out.rma.uni.r
@@ -30,6 +30,11 @@ leave1out.rma.uni <- function(x, digits, transf, targs, progbar=FALSE, ...) {
    if (missing(targs))
       targs <- NULL
 
+   funlist <- lapply(list(transf.exp.int, transf.ilogit.int, transf.ztor.int, transf.exp.mode, transf.ilogit.mode, transf.ztor.mode), deparse)
+
+   if (is.null(targs) && any(sapply(funlist, identical, deparse(transf))) && inherits(x, c("rma.uni","rma.glmm")) && length(x$tau2 == 1L))
+      targs <- c(tau2=x$tau2)
+
    ddd <- list(...)
 
    .chkdots(ddd, c("time"))

diff --git a/R/predict.rma.r b/R/predict.rma.r
@@ -52,6 +52,11 @@ level, adjust=FALSE, digits, transf, targs, vcov=FALSE, ...) {
    if (missing(targs))
       targs <- NULL
 
+   funlist <- lapply(list(transf.exp.int, transf.ilogit.int, transf.ztor.int, transf.exp.mode, transf.ilogit.mode, transf.ztor.mode), deparse)
+
+   if (is.null(targs) && any(sapply(funlist, identical, deparse(transf))) && inherits(x, c("rma.uni","rma.glmm")) && length(x$tau2 == 1L))
+      targs <- c(tau2=x$tau2)
+
    level <- .level(level)
 
    if (!is.logical(adjust))
@@ -543,9 +548,6 @@ level, adjust=FALSE, digits, transf, targs, vcov=FALSE, ...) {
    ### apply transformation function if one has been specified
 
    if (is.function(transf)) {
-      #funlist <- lapply(list(transf.exp.int, transf.ilogit.int, transf.ztor.int, transf.exp.mode, transf.ilogit.mode, transf.ztor.mode), deparse)
-      #if (is.null(targs) && any(sapply(funlist, identical, deparse(transf))) && inherits(x, c("rma.uni","rma.glmm")) && length(x$tau2 == 1L))
-      #   targs <- c(tau2=x$tau2)
       if (is.null(targs)) {
          pred  <- sapply(pred, transf)
          se    <- rep(NA_real_, k.new)

diff --git a/R/zzz.r b/R/zzz.r
@@ -1,6 +1,6 @@
 .onAttach <- function(libname, pkgname) {
 
-   ver <- "4.7-54"
+   ver <- "4.7-55"
 
    loadmsg <- paste0("\nLoading the 'metafor' package (version ", ver, "). For an\nintroduction to the package please type: help(metafor)\n")
 

diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@ metafor: A Meta-Analysis Package for R
 [![R build status](https://github.com/wviechtb/metafor/workflows/R-CMD-check/badge.svg)](https://github.com/wviechtb/metafor/actions)
 [![Code Coverage](https://codecov.io/gh/wviechtb/metafor/branch/master/graph/badge.svg)](https://app.codecov.io/gh/wviechtb/metafor)
 [![CRAN Version](https://www.r-pkg.org/badges/version/metafor)](https://cran.r-project.org/package=metafor)
-[![devel Version](https://img.shields.io/badge/devel-4.7--54-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version)
+[![devel Version](https://img.shields.io/badge/devel-4.7--55-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version)
 [![Monthly Downloads](https://cranlogs.r-pkg.org/badges/metafor)](https://cranlogs.r-pkg.org/badges/metafor)
 [![Total Downloads](https://cranlogs.r-pkg.org/badges/grand-total/metafor)](https://cranlogs.r-pkg.org/badges/grand-total/metafor)
 

diff --git a/docs/404.html b/docs/404.html
diff --git a/docs/ISSUE_TEMPLATE.html b/docs/ISSUE_TEMPLATE.html
diff --git a/docs/articles/index.html b/docs/articles/index.html
diff --git a/docs/articles/pkgdown/diagram.html b/docs/articles/pkgdown/diagram.html
diff --git a/docs/authors.html b/docs/authors.html
diff --git a/docs/index.html b/docs/index.html
diff --git a/docs/news/index.html b/docs/news/index.html
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
@@ -3,7 +3,7 @@ pkgdown: 2.1.1.9000
 pkgdown_sha: 0a18bc718640aee7160a0ebbcdef5ecaae2ac4a4
 articles:
   pkgdown/diagram: pkgdown/diagram.html
-last_built: 2024-11-21T16:31Z
+last_built: 2024-11-22T07:53Z
 urls:
   reference: https://wviechtb.github.io/metafor/reference
   article: https://wviechtb.github.io/metafor/articles
diff --git a/docs/reference/addpoly.default.html b/docs/reference/addpoly.default.html
diff --git a/docs/reference/addpoly.html b/docs/reference/addpoly.html
diff --git a/docs/reference/addpoly.predict.rma.html b/docs/reference/addpoly.predict.rma.html
diff --git a/docs/reference/addpoly.rma.html b/docs/reference/addpoly.rma.html
diff --git a/docs/reference/aggregate.escalc.html b/docs/reference/aggregate.escalc.html
diff --git a/docs/reference/anova.rma.html b/docs/reference/anova.rma.html
diff --git a/docs/reference/baujat.html b/docs/reference/baujat.html
diff --git a/docs/reference/bldiag.html b/docs/reference/bldiag.html
diff --git a/docs/reference/blsplit.html b/docs/reference/blsplit.html
diff --git a/docs/reference/blup.html b/docs/reference/blup.html
diff --git a/docs/reference/coef.permutest.rma.uni.html b/docs/reference/coef.permutest.rma.uni.html
diff --git a/docs/reference/coef.rma.html b/docs/reference/coef.rma.html
diff --git a/docs/reference/confint.rma.html b/docs/reference/confint.rma.html
diff --git a/docs/reference/contrmat.html b/docs/reference/contrmat.html
diff --git a/docs/reference/conv.2x2.html b/docs/reference/conv.2x2.html
diff --git a/docs/reference/conv.delta.html b/docs/reference/conv.delta.html
diff --git a/docs/reference/conv.fivenum.html b/docs/reference/conv.fivenum.html
diff --git a/docs/reference/conv.wald.html b/docs/reference/conv.wald.html