Minor fixes to the dynamic theming of plots.

wviechtb · Oct 22, 2023 · 23f5bc1 · 23f5bc1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metafor
-Version: 4.5-0
-Date: 2023-10-01
+Version: 4.5-1
+Date: 2023-10-22
 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
@@ -1,6 +1,6 @@
-# metafor 4.5-0 (2023-10-01)
+# metafor 4.5-1 (2023-10-22)
 
-- bump for devel version
+- a few minor fixes to the dynamic theming of plots based on the foreground and background colors of the plotting device
 
 # metafor 4.4-0 (2023-09-27)
 

diff --git a/R/anova.rma.r b/R/anova.rma.r
@@ -294,7 +294,7 @@ anova.rma <- function(object, object2, btt, X, att, Z, rhs, digits, refit=FALSE,
                ddf <- cs.lc$df
 
                if (!missing(rhs))
-                  warning(mstyle$warning("Cannot use 'rhs' argument for 'robust.rma' objects based on 'clubSandwich'."))
+                  warning(mstyle$warning("Cannot use 'rhs' argument for 'robust.rma' objects based on 'clubSandwich'."), call.=FALSE)
 
                rhs <- rep(0, m)
 
@@ -504,7 +504,7 @@ anova.rma <- function(object, object2, btt, X, att, Z, rhs, digits, refit=FALSE,
       ### for LRTs, using anything besides ML/REML is strictly speaking incorrect
 
       if (test == "LRT" && (!is.element(model.f$method, c("FE","EE","CE","ML","REML")) || !is.element(model.r$method, c("FE","EE","CE","ML","REML"))))
-         warning(mstyle$warning("LRTs should be based on ML/REML estimation."))
+         warning(mstyle$warning("LRTs should be based on ML/REML estimation."), call.=FALSE)
 
       ### for LRTs based on REML estimation, check if fixed effects differ
       if (test == "LRT" && model.f$method == "REML" && (!identical(model.f$X, model.r$X))) {

diff --git a/R/emmprep.r b/R/emmprep.r
@@ -113,7 +113,7 @@ emmprep <- function(x, verbose=FALSE, ...) {
 
    if (is.null(ddd$tran)) {
 
-      if (is.element(x$measure, c("RR","OR","MPORM","PETO","MPRR","MPOR","MPORC","MPPETO","IRR","ROM","D2OR","D2ORL","D2ORN","CVR","VR","PLN","IRLN","SDLN","MNLN","CVLN","ROMC","CVRC","VRC","REH"))) {
+      if (is.element(x$measure, c("RR","OR","MPORM","PETO","MPRR","MPOR","MPORC","MPPETO","IRR","ROM","D2OR","D2ORL","D2ORN","CVR","VR","PLN","IRLN","SDLN","MNLN","CVLN","ROMC","CVRC","VRC","REH","HRR"))) {
          out@misc$tran <- "log"
          #out@misc$tran <- emmeans::make.tran("genlog", 0)
          #out <- update(out, emmeans::make.tran("genlog", 0))

diff --git a/R/escalc.r b/R/escalc.r
@@ -30,6 +30,7 @@ data, slab, subset, include, add=1/2, to="only0", drop00=FALSE, vtype="LS", var.
                               "MC","SMCC","SMCR","SMCRH","ROMC","CVRC","VRC",      # raw/standardized mean change, log(ROM), CVR, and VR for dependent samples
                               "ARAW","AHW","ABT",                                  # alpha (and transformations thereof)
                               "REH",                                               # relative excess heterozygosity
+                              "HRR","HRD",                                         # hazard rate ratios and differences
                               "GEN")))
       stop(mstyle$stop("Unknown 'measure' specified."))
 

diff --git a/R/funnel.default.r b/R/funnel.default.r
@@ -38,7 +38,7 @@ label=FALSE, offset=0.4, legend=FALSE, ...) {
       shade <- rep(shade, length(level))
 
    if (missing(hlines))
-      hlines <- par("bg")
+      hlines <- .coladj(par("bg","fg"), dark=c(0,-0.9), light=c(0,1))
 
    if (is.null(refline))
       refline <- NA
@@ -592,11 +592,6 @@ label=FALSE, offset=0.4, legend=FALSE, ...) {
 
    #########################################################################
 
-   ### add L-shaped box around plot
-
-   if (!is.na(colbox))
-      box(bty="l", col=colbox)
-
    ### generate x-axis positions if none are specified
 
    if (is.null(at)) {
@@ -624,6 +619,11 @@ label=FALSE, offset=0.4, legend=FALSE, ...) {
 
    laxis(side=1, at=at, labels=at.lab, ...)
 
+   ### add L-shaped box around plot
+
+   if (!is.na(colbox))
+      box(bty="l", col=colbox)
+
    ############################################################################
 
    ### labeling of points

diff --git a/R/funnel.rma.r b/R/funnel.rma.r
@@ -38,7 +38,7 @@ label=FALSE, offset=0.4, legend=FALSE, ...) {
       shade <- rep(shade, length(level))
 
    if (missing(hlines))
-      hlines <- par("bg")
+      hlines <- .coladj(par("bg","fg"), dark=c(0,-0.8), light=c(0,1))
 
    if (!missing(refline) && is.null(refline))
       refline <- NA
@@ -639,11 +639,6 @@ label=FALSE, offset=0.4, legend=FALSE, ...) {
 
    #########################################################################
 
-   ### add L-shaped box around plot
-
-   if (!is.na(colbox))
-      box(bty="l", col=colbox)
-
    ### generate x-axis positions if none are specified
 
    if (is.null(at)) {
@@ -671,6 +666,11 @@ label=FALSE, offset=0.4, legend=FALSE, ...) {
 
    laxis(side=1, at=at, labels=at.lab, ...)
 
+   ### add L-shaped box around plot
+
+   if (!is.na(colbox))
+      box(bty="l", col=colbox)
+
    ############################################################################
 
    ### labeling of points

diff --git a/R/misc.func.hidden.funnel.r b/R/misc.func.hidden.funnel.r
@@ -8,7 +8,7 @@
                  y         = NULL,
                  inset     = 0.01,
                  bty       = "o",
-                 bg        = .coladj(par("bg","fg"), dark=0.00, light=0.00), # avoids a transparent background
+                 bg        = .coladj(par("bg","fg"), dark=c(0,-0.9), light=c(0,0.9)),
                  studies   = TRUE,
                  show      = "pvals",
                  cex       = c(1,2,1),

diff --git a/R/misc.func.hidden.r b/R/misc.func.hidden.r
@@ -1083,6 +1083,26 @@
          }
       }
       ######################################################################
+      if (measure == "HRR") {
+         if (identical(transf.char, "FALSE") && identical(atransf.char, "FALSE")) {
+            lab <- ifelse(short, "Log[HR]", "Log Hazard Ratio")
+         } else {
+            lab <- ifelse(short, lab, "Transformed Log Hazard Ratio")
+            funlist <- lapply(list(exp, transf.exp.int), deparse)
+            if (any(sapply(funlist, identical, atransf.char)))
+               lab <- ifelse(short, "REH", "Hazard Ratio (log scale)")
+            if (any(sapply(funlist, identical, transf.char)))
+               lab <- ifelse(short, "REH", "Hazard Ratio")
+         }
+      }
+      if (measure == "HRD") {
+         if (identical(transf.char, "FALSE") && identical(atransf.char, "FALSE")) {
+            lab <- ifelse(short, "HR Difference", "Hazard Rate Difference")
+         } else {
+            lab <- ifelse(short, lab, "Transformed Hazard Rate Difference")
+         }
+      }
+      ######################################################################
 
    }
 
@@ -1854,6 +1874,7 @@
    } else {
       col <- col + round(light*255)[[pos]]
    }
+
    col[col < 0] <- 0
    col[col > 255] <- 255
 

diff --git a/R/plot.permutest.rma.uni.r b/R/plot.permutest.rma.uni.r
@@ -177,7 +177,7 @@ plot.permutest.rma.uni <- function(x, beta, alpha, QM=FALSE, QS=FALSE,
          ltys  <- ltys[lwds > 0]
          #pchs  <- pchs[lwds > 0]
          lwds  <- lwds[lwds > 0]
-         legend(lpos, inset=.01, bg=par("bg"), lwd=lwds, col=lcols, lty=ltys, legend=ltxt)
+         legend(lpos, inset=.01, bg=.coladj(par("bg"), dark=0, light=0), lwd=lwds, col=lcols, lty=ltys, legend=ltxt)
 
       }
 

diff --git a/R/regplot.rma.r b/R/regplot.rma.r
@@ -791,7 +791,7 @@ lcol, lwd, lty, legend=FALSE, xvals, ...) {
       }
 
       if (length(ltxt) >= 1L)
-         legend(lpos, inset=.01, bg=par("bg"), pch=pch.l, col=col.l, pt.bg=bg.l, lty=lty.l, lwd=lwd.l, text.col=tcol.l, pt.cex=1.5, seg.len=3, legend=ltxt, box.lty=box.lty)
+         legend(lpos, inset=.01, bg=.coladj(par("bg"), dark=0, light=0), pch=pch.l, col=col.l, pt.bg=bg.l, lty=lty.l, lwd=lwd.l, text.col=tcol.l, pt.cex=1.5, seg.len=3, legend=ltxt, box.lty=box.lty)
 
       pch.l  <- NULL
       col.l  <- NULL

diff --git a/R/rma.uni.r b/R/rma.uni.r
@@ -30,6 +30,7 @@ test="z", level=95, btt, att, tau2, verbose=FALSE, digits, control, ...) {
                               "MC","SMCC","SMCR","SMCRH","ROMC","CVRC","VRC",      # raw/standardized mean change, log(ROM), CVR, and VR for dependent samples
                               "ARAW","AHW","ABT",                                  # alpha (and transformations thereof)
                               "REH",                                               # relative excess heterozygosity
+                              "HRR","HRD",                                         # hazard rate ratios and differences
                               "GEN")))
       stop(mstyle$stop("Unknown 'measure' specified."))
 

diff --git a/R/zzz.r b/R/zzz.r
@@ -1,6 +1,6 @@
 .onAttach <- function(libname, pkgname) {
 
-   ver <- "4.5-0"
+   ver <- "4.5-1"
 
    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-4.5--0-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version)
+[![devel Version](https://img.shields.io/badge/devel-4.5--1-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: 2.0.7
 pkgdown_sha: ~
 articles:
   diagram: pkgdown/diagram.html
-last_built: 2023-10-01T10:20Z
+last_built: 2023-10-22T14:05Z
 urls:
   reference: https://wviechtb.github.io/metafor/reference
   article: https://wviechtb.github.io/metafor/articles

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