Added 'pval' argument to selmodel().

wviechtb · Mar 18, 2024 · 1d41d13 · 1d41d13
1 parent 74413fa
commit 1d41d13
Show file tree

Hide file tree

Showing 123 changed files with 167 additions and 138 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metafor
-Version: 4.5-10
-Date: 2024-03-07
+Version: 4.5-11
+Date: 2024-03-18
 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"))
 Depends: R (>= 4.0.0), methods, Matrix, metadat, numDeriv

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# metafor 4.5-10 (2024-03-07)
+# metafor 4.5-11 (2024-03-18)
 
 - the `steps` argument in the various `profile()` functions can now also be a numeric vector to specify for which parameter values the likelihood should be evaluated
 
@@ -16,6 +16,8 @@
 
 - in `forest()` and `regplot()`, observation limits set via `olim` are now properly applied to all elements
 
+- added the undocumented argument `pval` to `selmodel()` for passing p-values directly to the function (doing this is highly experimental)
+
 - some internal refactoring of the code
 
 - improved the documentation a bit

diff --git a/R/selmodel.rma.uni.r b/R/selmodel.rma.uni.r
@@ -57,7 +57,7 @@ selmodel.rma.uni <- function(x, type, alternative="greater", prec, delta, steps,
 
    ddd <- list(...)
 
-   .chkdots(ddd, c("time", "tau2", "beta", "skiphes", "skiphet", "skipintcheck", "scaleprec", "defmap", "mapfun", "mapinvfun"))
+   .chkdots(ddd, c("time", "tau2", "beta", "skiphes", "skiphet", "skipintcheck", "scaleprec", "defmap", "mapfun", "mapinvfun", "pval"))
 
    ### handle 'tau2' argument from ...
 
@@ -137,7 +137,25 @@ selmodel.rma.uni <- function(x, type, alternative="greater", prec, delta, steps,
 
    ### compute p-values
 
-   pvals <- .selmodel.pval(yi=yi, vi=vi, alternative=alternative)
+   if (is.null(ddd$pval)) {
+
+      pvals <- .selmodel.pval(yi=yi, vi=vi, alternative=alternative)
+
+   } else {
+
+      pvals <- ddd$pval
+
+      if (length(pvals) != x$k.all)
+         stop(mstyle$stop(paste0("Length of the 'pval' argument (", length(pvals), ") does not correspond to the size of the original dataset (", x$k.all, ").")))
+
+      pvals <- .getsubset(pvals, x$subset)
+
+      if (anyNA(pvals))
+         stop(mstyle$stop(paste0("No missing values in 'pval' argument allowed.")))
+      if (any(pvals <= 0) || any(pvals > 1))
+         stop(mstyle$stop(paste0("One or more 'pval' values are <= 0 or > 1.")))
+
+   }
 
    ### checks on steps argument
 
@@ -158,8 +176,12 @@ selmodel.rma.uni <- function(x, type, alternative="greater", prec, delta, steps,
 
       steps <- unique(sort(steps))
 
-      if (type != "trunc" && steps[length(steps)] != 1)
-         steps <- c(steps, 1)
+      if (type != "trunc") {
+         if (steps[1] == 0)
+            stop(mstyle$stop("Lowest 'steps' value must be > 0."))
+         if (steps[length(steps)] != 1)
+            steps <- c(steps, 1)
+      }
 
    }
 

diff --git a/R/zzz.r b/R/zzz.r
@@ -1,6 +1,6 @@
 .onAttach <- function(libname, pkgname) {
 
-   ver <- "4.5-10"
+   ver <- "4.5-11"
 
    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--10-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version)
+[![devel Version](https://img.shields.io/badge/devel-4.5--11-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: 2024-03-07T09:57Z
+last_built: 2024-03-18T11:24Z
 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