Avoid problems with profile() and confint() when metafor is not direc…

…tly loaded.
wviechtb · Oct 28, 2024 · 9ddf439 · 9ddf439
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: metafor
-Version: 4.7-41
+Version: 4.7-42
 Date: 2024-10-28
 Title: Meta-Analysis Package for R
 Authors@R: person(given = "Wolfgang", family = "Viechtbauer", role = c("aut","cre"), email = "wvb@metafor-project.org", comment = c(ORCID = "0000-0003-3463-4063"))

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# metafor 4.7-41 (2024-10-28)
+# metafor 4.7-42 (2024-10-28)
 
 - 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.ls.r b/R/confint.rma.ls.r
@@ -76,6 +76,7 @@ confint.rma.ls <- function(object, parm, level, fixed=FALSE, alpha, digits, tran
             cl.vc$alpha <- pos
             cl.vc$time <- FALSE
             #cl.vc$object <- quote(x)
+            cl.vc[[1]] <- str2lang("metafor::confint.rma.ls")
             if (verbose)
                cat(mstyle$verbose(paste("\nObtaining CI for alpha =", pos, "\n")))
             res.all[[j]] <- eval(cl.vc, envir=parent.frame())

diff --git a/R/confint.rma.mv.r b/R/confint.rma.mv.r
@@ -75,6 +75,7 @@ confint.rma.mv <- function(object, parm, level, fixed=FALSE, sigma2, tau2, rho,
             cl.vc$sigma2 <- pos
             cl.vc$time <- FALSE
             #cl.vc$object <- quote(x)
+            cl.vc[[1]] <- str2lang("metafor::confint.rma.mv")
             if (verbose)
                cat(mstyle$verbose(paste("\nObtaining CI for sigma2 =", pos, "\n")))
             res.all[[j]] <- eval(cl.vc, envir=parent.frame())
@@ -89,6 +90,7 @@ confint.rma.mv <- function(object, parm, level, fixed=FALSE, sigma2, tau2, rho,
                cl.vc$tau2 <- pos
                cl.vc$time <- FALSE
                #cl.vc$object <- quote(x)
+               cl.vc[[1]] <- str2lang("metafor::confint.rma.mv")
                if (verbose)
                   cat(mstyle$verbose(paste("\nObtaining CI for tau2 =", pos, "\n")))
                res.all[[j]] <- eval(cl.vc, envir=parent.frame())
@@ -101,6 +103,7 @@ confint.rma.mv <- function(object, parm, level, fixed=FALSE, sigma2, tau2, rho,
                cl.vc$rho <- pos
                cl.vc$time <- FALSE
                #cl.vc$object <- quote(x)
+               cl.vc[[1]] <- str2lang("metafor::confint.rma.mv")
                if (verbose)
                   cat(mstyle$verbose(paste("\nObtaining CI for rho =", pos, "\n")))
                res.all[[j]] <- eval(cl.vc, envir=parent.frame())
@@ -116,6 +119,7 @@ confint.rma.mv <- function(object, parm, level, fixed=FALSE, sigma2, tau2, rho,
                cl.vc$gamma2 <- pos
                cl.vc$time <- FALSE
                #cl.vc$object <- quote(x)
+               cl.vc[[1]] <- str2lang("metafor::confint.rma.mv")
                if (verbose)
                   cat(mstyle$verbose(paste("\nObtaining CI for gamma2 =", pos, "\n")))
                res.all[[j]] <- eval(cl.vc, envir=parent.frame())
@@ -128,6 +132,7 @@ confint.rma.mv <- function(object, parm, level, fixed=FALSE, sigma2, tau2, rho,
                cl.vc$phi <- pos
                cl.vc$time <- FALSE
                #cl.vc$object <- quote(x)
+               cl.vc[[1]] <- str2lang("metafor::confint.rma.mv")
                if (verbose)
                   cat(mstyle$verbose(paste("\nObtaining CI for phi =", pos, "\n")))
                res.all[[j]] <- eval(cl.vc, envir=parent.frame())

diff --git a/R/confint.rma.uni.selmodel.r b/R/confint.rma.uni.selmodel.r
@@ -78,6 +78,7 @@ confint.rma.uni.selmodel <- function(object, parm, level, fixed=FALSE, tau2, del
          cl.vc$tau2 <- 1
          cl.vc$time <- FALSE
          #cl.vc$object <- quote(x)
+         cl.vc[[1]] <- str2lang("metafor::confint.rma.uni.selmodel")
          if (verbose)
             cat(mstyle$verbose(paste("\nObtaining CI for tau2\n")))
          res.all[[j]] <- eval(cl.vc, envir=parent.frame())
@@ -90,6 +91,7 @@ confint.rma.uni.selmodel <- function(object, parm, level, fixed=FALSE, tau2, del
             cl.vc$delta <- pos
             cl.vc$time <- FALSE
             #cl.vc$object <- quote(x)
+            cl.vc[[1]] <- str2lang("metafor::confint.rma.uni.selmodel")
             if (verbose)
                cat(mstyle$verbose(paste("\nObtaining CI for delta =", pos, "\n")))
             res.all[[j]] <- eval(cl.vc, envir=parent.frame())

diff --git a/R/profile.rma.ls.r b/R/profile.rma.ls.r
@@ -96,6 +96,7 @@ profile.rma.ls <- function(fitted, alpha,
             mc.vc$alpha <- pos
             mc.vc$time <- FALSE
             #mc.vc$fitted <- quote(x)
+            mc.vc[[1]] <- str2lang("metafor::profile.rma.ls")
             if (progbar)
                cat(mstyle$verbose(paste("Profiling alpha =", pos, "\n")))
             sav[[j]] <- eval(mc.vc, envir=parent.frame())

diff --git a/R/profile.rma.mv.r b/R/profile.rma.mv.r
@@ -96,6 +96,7 @@ profile.rma.mv <- function(fitted, sigma2, tau2, rho, gamma2, phi,
             mc.vc$sigma2 <- pos
             mc.vc$time <- FALSE
             #mc.vc$fitted <- quote(x)
+            mc.vc[[1]] <- str2lang("metafor::profile.rma.mv")
             if (progbar)
                cat(mstyle$verbose(paste("Profiling sigma2 =", pos, "\n")))
             sav[[j]] <- eval(mc.vc, envir=parent.frame())
@@ -110,6 +111,7 @@ profile.rma.mv <- function(fitted, sigma2, tau2, rho, gamma2, phi,
                mc.vc$tau2 <- pos
                mc.vc$time <- FALSE
                #mc.vc$fitted <- quote(x)
+               mc.vc[[1]] <- str2lang("metafor::profile.rma.mv")
                if (progbar)
                   cat(mstyle$verbose(paste("Profiling tau2 =", pos, "\n")))
                sav[[j]] <- eval(mc.vc, envir=parent.frame())
@@ -122,6 +124,7 @@ profile.rma.mv <- function(fitted, sigma2, tau2, rho, gamma2, phi,
                mc.vc$rho <- pos
                mc.vc$time <- FALSE
                #mc.vc$fitted <- quote(x)
+               mc.vc[[1]] <- str2lang("metafor::profile.rma.mv")
                if (progbar)
                   cat(mstyle$verbose(paste("Profiling rho =", pos, "\n")))
                sav[[j]] <- eval(mc.vc, envir=parent.frame())
@@ -137,6 +140,7 @@ profile.rma.mv <- function(fitted, sigma2, tau2, rho, gamma2, phi,
                mc.vc$gamma2 <- pos
                mc.vc$time <- FALSE
                #mc.vc$fitted <- quote(x)
+               mc.vc[[1]] <- str2lang("metafor::profile.rma.mv")
                if (progbar)
                   cat(mstyle$verbose(paste("Profiling gamma2 =", pos, "\n")))
                sav[[j]] <- eval(mc.vc, envir=parent.frame())
@@ -149,6 +153,7 @@ profile.rma.mv <- function(fitted, sigma2, tau2, rho, gamma2, phi,
                mc.vc$phi <- pos
                mc.vc$time <- FALSE
                #mc.vc$fitted <- quote(x)
+               mc.vc[[1]] <- str2lang("metafor::profile.rma.mv")
                if (progbar)
                   cat(mstyle$verbose(paste("Profiling phi =", pos, "\n")))
                sav[[j]] <- eval(mc.vc, envir=parent.frame())

diff --git a/R/profile.rma.uni.selmodel.r b/R/profile.rma.uni.selmodel.r
@@ -95,6 +95,7 @@ profile.rma.uni.selmodel <- function(fitted, tau2, delta,
          mc.vc$tau2 <- 1
          mc.vc$time <- FALSE
          #mc.vc$fitted <- quote(x)
+         mc.vc[[1]] <- str2lang("metafor::profile.rma.uni.selmodel")
          if (progbar)
             cat(mstyle$verbose(paste("Profiling tau2\n")))
          sav[[j]] <- eval(mc.vc, envir=parent.frame())
@@ -107,6 +108,7 @@ profile.rma.uni.selmodel <- function(fitted, tau2, delta,
             mc.vc$delta <- pos
             mc.vc$time <- FALSE
             #mc.vc$fitted <- quote(x)
+            mc.vc[[1]] <- str2lang("metafor::profile.rma.uni.selmodel")
             if (progbar)
                cat(mstyle$verbose(paste("Profiling delta =", pos, "\n")))
             sav[[j]] <- eval(mc.vc, envir=parent.frame())

diff --git a/R/rma.mv.r b/R/rma.mv.r
@@ -775,7 +775,7 @@ cvvc=FALSE, sparse=FALSE, verbose=FALSE, digits, control, ...) {
 
    }
 
-   mf.r <- unname(mf.r)
+   mf.r <- unname(mf.r) # to avoid problems when list elements in 'random' are named
 
    ### warn that 'struct' argument is disregarded if it has been specified, but model contains no '~ inner | outer' terms
 

diff --git a/R/zzz.r b/R/zzz.r
@@ -1,6 +1,6 @@
 .onAttach <- function(libname, pkgname) {
 
-   ver <- "4.7-41"
+   ver <- "4.7-42"
 
    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--41-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version)
+[![devel Version](https://img.shields.io/badge/devel-4.7--42-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: 2024-10-28T07:24Z
+last_built: 2024-10-28T15:03Z
 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