Added 'ilab.lab' argument to the various forest() functions.

wviechtb · Jun 7, 2024 · feacbe6 · feacbe6
1 parent c805881
commit feacbe6
Show file tree

Hide file tree

Showing 131 changed files with 268 additions and 256 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metafor
-Version: 4.7-13
-Date: 2024-05-31
+Version: 4.7-14
+Date: 2024-06-07
 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 4.7-13 (2024-05-31)
+# metafor 4.7-14 (2024-06-07)
 
 - `rma.mv()` now counts the number of levels of a random effect more appropriately; this may trigger more often the check whether the number of levels is equal to 1, in which case the corresponding variance component is automatically fixed to 0; this check can be omitted with `control=list(check.k.gtr.1=FALSE)`
 
@@ -10,6 +10,8 @@
 
 - added `lim`, `ci`, `pi`, `legend`, and `flip` arguments to `labbe()`
 
+- added `ilab.lab` argument to the various `forest()` functions
+
 - `fsn(..., type="General")` now computes the final estimates after rounding the fail-safe N value (not before)
 
 - added more tests

diff --git a/R/forest.cumul.rma.r b/R/forest.cumul.rma.r
@@ -1,9 +1,9 @@
 forest.cumul.rma <- function(x,
 annotate=TRUE,                                                header=FALSE,
 xlim, alim, olim, ylim, at, steps=5, level=x$level, refline=0, digits=2L, width,
-xlab,             ilab, ilab.xpos, ilab.pos,
+xlab,             ilab, ilab.lab, ilab.xpos, ilab.pos,
 transf, atransf, targs, rows,
-efac=1, pch, psize,                           col,         shade, colshade,
+efac=1, pch, psize,                          col,         shade, colshade,
 lty, fonts, cex, cex.lab, cex.axis, ...) {
 
    #########################################################################
@@ -47,6 +47,9 @@ lty, fonts, cex, cex.lab, cex.axis, ...) {
       ilab <- .getx("ilab", mf=mf, data=x$data)
    }
 
+   if (missing(ilab.lab))
+      ilab.lab <- NULL
+
    if (missing(ilab.xpos))
       ilab.xpos <- NULL
 
@@ -706,13 +709,17 @@ lty, fonts, cex, cex.lab, cex.axis, ...) {
          if (ncol.ilab >= 4L)
             ilab.xpos <- seq(xlim[1] + dist*0.5, xlim[1] + dist*0.9, length.out=ncol.ilab)
       }
-      if (length(ilab.xpos) != ncol(ilab))
-         stop(mstyle$stop(paste0("Number of 'ilab' columns (", ncol(ilab), ") does not match length of 'ilab.xpos' argument (", length(ilab.xpos), ").")))
+      if (length(ilab.xpos) != ncol.ilab)
+         stop(mstyle$stop(paste0("Number of 'ilab' columns (", ncol.ilab, ") does not match length of 'ilab.xpos' argument (", length(ilab.xpos), ").")))
       if (!is.null(ilab.pos) && length(ilab.pos) == 1L)
-         ilab.pos <- rep(ilab.pos, ncol(ilab))
+         ilab.pos <- rep(ilab.pos, ncol.ilab)
+      if (!is.null(ilab.lab) && length(ilab.lab) != ncol.ilab)
+         stop(mstyle$stop(paste0("Number of 'ilab' columns (", ncol.ilab, ") does not match length of 'ilab.lab' argument (", length(ilab.lab), ").")))
       par(family=names(fonts)[3], font=fonts[3])
-      for (l in seq_len(ncol(ilab))) {
+      for (l in seq_len(ncol.ilab)) {
          ltext(ilab.xpos[l], rows+rowadj[3], ilab[,l], pos=ilab.pos[l], cex=cex, ...)
+         if (!is.null(ilab.lab))
+            ltext(ilab.xpos[l], ylim[2]-(top-1)+1+rowadj[3], ilab.lab[l], pos=ilab.pos[l], font=2, cex=cex, ...)
       }
       par(family=names(fonts)[1], font=fonts[1])
    }
@@ -785,8 +792,8 @@ lty, fonts, cex, cex.lab, cex.axis, ...) {
 
    ### add header
 
-   ltext(textpos[1], ylim[2]-(top-1)+1, header.left,  pos=4, font=2, cex=cex, ...)
-   ltext(textpos[2], ylim[2]-(top-1)+1, header.right, pos=2, font=2, cex=cex, ...)
+   ltext(textpos[1], ylim[2]-(top-1)+1+rowadj[1], header.left,  pos=4, font=2, cex=cex, ...)
+   ltext(textpos[2], ylim[2]-(top-1)+1+rowadj[2], header.right, pos=2, font=2, cex=cex, ...)
 
    #########################################################################
 

diff --git a/R/forest.default.r b/R/forest.default.r
@@ -1,7 +1,7 @@
 forest.default   <- function(x, vi, sei, ci.lb, ci.ub,
 annotate=TRUE,                             showweights=FALSE, header=FALSE,
 xlim, alim, olim, ylim, at, steps=5, level=95,      refline=0, digits=2L, width,
-xlab, slab,       ilab, ilab.xpos, ilab.pos, order, subset,
+xlab, slab,       ilab, ilab.lab, ilab.xpos, ilab.pos, order, subset,
 transf, atransf, targs, rows,
 efac=1, pch, psize, plim=c(0.5,1.5),         col,         shade, colshade,
 lty, fonts, cex, cex.lab, cex.axis, ...) {
@@ -40,6 +40,9 @@ lty, fonts, cex, cex.lab, cex.axis, ...) {
    if (missing(ilab))
       ilab <- NULL
 
+   if (missing(ilab.lab))
+      ilab.lab <- NULL
+
    if (missing(ilab.xpos))
       ilab.xpos <- NULL
 
@@ -847,13 +850,17 @@ lty, fonts, cex, cex.lab, cex.axis, ...) {
          if (ncol.ilab >= 4L)
             ilab.xpos <- seq(xlim[1] + dist*0.5, xlim[1] + dist*0.9, length.out=ncol.ilab)
       }
-      if (length(ilab.xpos) != ncol(ilab))
-         stop(mstyle$stop(paste0("Number of 'ilab' columns (", ncol(ilab), ") does not match length of 'ilab.xpos' argument (", length(ilab.xpos), ").")))
+      if (length(ilab.xpos) != ncol.ilab)
+         stop(mstyle$stop(paste0("Number of 'ilab' columns (", ncol.ilab, ") does not match length of 'ilab.xpos' argument (", length(ilab.xpos), ").")))
       if (!is.null(ilab.pos) && length(ilab.pos) == 1L)
-         ilab.pos <- rep(ilab.pos, ncol(ilab))
+         ilab.pos <- rep(ilab.pos, ncol.ilab)
+      if (!is.null(ilab.lab) && length(ilab.lab) != ncol.ilab)
+         stop(mstyle$stop(paste0("Number of 'ilab' columns (", ncol.ilab, ") does not match length of 'ilab.lab' argument (", length(ilab.lab), ").")))
       par(family=names(fonts)[3], font=fonts[3])
-      for (l in seq_len(ncol(ilab))) {
+      for (l in seq_len(ncol.ilab)) {
          ltext(ilab.xpos[l], rows+rowadj[3], ilab[,l], pos=ilab.pos[l], cex=cex, ...)
+         if (!is.null(ilab.lab))
+            ltext(ilab.xpos[l], ylim[2]-(top-1)+1+rowadj[3], ilab.lab[l], pos=ilab.pos[l], font=2, cex=cex, ...)
       }
       par(family=names(fonts)[1], font=fonts[1])
    }
@@ -935,8 +942,8 @@ lty, fonts, cex, cex.lab, cex.axis, ...) {
 
    ### add header
 
-   ltext(textpos[1], ylim[2]-(top-1)+1, header.left,  pos=4, font=2, cex=cex, ...)
-   ltext(textpos[2], ylim[2]-(top-1)+1, header.right, pos=2, font=2, cex=cex, ...)
+   ltext(textpos[1], ylim[2]-(top-1)+1+rowadj[1], header.left,  pos=4, font=2, cex=cex, ...)
+   ltext(textpos[2], ylim[2]-(top-1)+1+rowadj[2], header.right, pos=2, font=2, cex=cex, ...)
 
    #########################################################################
 

diff --git a/R/forest.rma.r b/R/forest.rma.r
@@ -1,7 +1,7 @@
 forest.rma       <- function(x,
 annotate=TRUE, addfit=TRUE, addpred=FALSE, showweights=FALSE, header=FALSE,
 xlim, alim, olim, ylim, at, steps=5, level=x$level, refline=0, digits=2L, width,
-xlab, slab, mlab, ilab, ilab.xpos, ilab.pos, order,
+xlab, slab, mlab, ilab, ilab.lab, ilab.xpos, ilab.pos, order,
 transf, atransf, targs, rows,
 efac=1, pch, psize, plim=c(0.5,1.5), colout, col, border, shade, colshade,
 lty, fonts, cex, cex.lab, cex.axis, ...) {
@@ -46,6 +46,9 @@ lty, fonts, cex, cex.lab, cex.axis, ...) {
       ilab <- .getx("ilab", mf=mf, data=x$data)
    }
 
+   if (missing(ilab.lab))
+      ilab.lab <- NULL
+
    if (missing(ilab.xpos))
       ilab.xpos <- NULL
 
@@ -1097,9 +1100,13 @@ lty, fonts, cex, cex.lab, cex.axis, ...) {
          stop(mstyle$stop(paste0("Number of 'ilab' columns (", ncol.ilab, ") does not match length of 'ilab.xpos' argument (", length(ilab.xpos), ").")))
       if (!is.null(ilab.pos) && length(ilab.pos) == 1L)
          ilab.pos <- rep(ilab.pos, ncol.ilab)
+      if (!is.null(ilab.lab) && length(ilab.lab) != ncol.ilab)
+         stop(mstyle$stop(paste0("Number of 'ilab' columns (", ncol.ilab, ") does not match length of 'ilab.lab' argument (", length(ilab.lab), ").")))
       par(family=names(fonts)[3], font=fonts[3])
       for (l in seq_len(ncol.ilab)) {
          ltext(ilab.xpos[l], rows+rowadj[3], ilab[,l], pos=ilab.pos[l], cex=cex, ...)
+         if (!is.null(ilab.lab))
+            ltext(ilab.xpos[l], ylim[2]-(top-1)+1+rowadj[3], ilab.lab[l], pos=ilab.pos[l], font=2, cex=cex, ...)
       }
       par(family=names(fonts)[1], font=fonts[1])
    }
@@ -1216,8 +1223,8 @@ lty, fonts, cex, cex.lab, cex.axis, ...) {
 
    ### add header
 
-   ltext(textpos[1], ylim[2]-(top-1)+1, header.left,  pos=4, font=2, cex=cex, ...)
-   ltext(textpos[2], ylim[2]-(top-1)+1, header.right, pos=2, font=2, cex=cex, ...)
+   ltext(textpos[1], ylim[2]-(top-1)+1+rowadj[1], header.left,  pos=4, font=2, cex=cex, ...)
+   ltext(textpos[2], ylim[2]-(top-1)+1+rowadj[2], header.right, pos=2, font=2, cex=cex, ...)
 
    #########################################################################
 

diff --git a/R/zzz.r b/R/zzz.r
@@ -1,6 +1,6 @@
 .onAttach <- function(libname, pkgname) {
 
-   ver <- "4.7-13"
+   ver <- "4.7-14"
 
    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--13-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version)
+[![devel Version](https://img.shields.io/badge/devel-4.7--14-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: 2.0.9
 pkgdown_sha: ~
 articles:
   diagram: pkgdown/diagram.html
-last_built: 2024-05-31T10:15Z
+last_built: 2024-06-07T12:42Z
 urls:
   reference: https://wviechtb.github.io/metafor/reference
   article: https://wviechtb.github.io/metafor/articles

diff --git a/docs/reference/addpoly.default-1.png b/docs/reference/addpoly.default-1.png