Added se() extractor function.

wviechtb · Apr 12, 2024 · f9dc9fb · f9dc9fb
1 parent 30a8013
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: metafor
-Version: 4.7-2
-Date: 2024-04-10
+Version: 4.7-3
+Date: 2024-04-12
 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/NAMESPACE b/NAMESPACE
@@ -142,6 +142,8 @@ S3method(rstudent, rma.mh)
 S3method(rstudent, rma.mv)
 S3method(rstudent, rma.peto)
 S3method(rstudent, rma.uni)
+S3method(se, default)
+S3method(se, rma)
 S3method(simulate, rma)
 S3method(summary, escalc)
 S3method(summary, matreg)

diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,9 @@
-# metafor 4.7-2 (2024-04-10)
+# metafor 4.7-3 (2024-04-12)
 
 - argument `shade` in `funnel()` now automatically uses a color gradient for the regions when multiple `level` values are specified
 
+- added extractor for function `se()` for extracting standard errors from model objects
+
 - added more tests
 
 # metafor 4.6-0 (2024-03-28)

diff --git a/R/se.r b/R/se.r
@@ -0,0 +1,53 @@
+se <- function(object, ...)
+   UseMethod("se")
+
+se.default <- function(object, ...) {
+
+   mstyle <- .get.mstyle()
+
+   vb <- try(vcov(object, ...), silent=TRUE)
+
+   if (inherits(vb, "try-error") || !is.matrix(vb) || !.is.square(vb))
+      stop(mstyle$stop("Default method for extracting the standard errors does not work for such model objects."))
+
+   return(sqrt(diag(vb)))
+
+}
+
+se.rma <- function(object, ...) {
+
+   mstyle <- .get.mstyle()
+
+   .chkclass(class(object), must="rma")
+
+   ddd <- list(...)
+
+   ses <- c(object$se)
+   names(ses) <- rownames(object$beta)
+
+   if (isTRUE(ddd$type=="beta"))
+      return(ses)
+
+   if (inherits(object, "rma.ls")) {
+      ses <- list(beta=ses)
+      ses$alpha <- c(object$se.alpha)
+      names(ses$alpha) <- rownames(object$alpha)
+      if (isTRUE(ddd$type=="alpha"))
+         return(ses$alpha)
+   }
+
+   if (inherits(object, "rma.uni.selmodel")) {
+      ses <- list(beta=ses)
+      ses$delta <- c(object$se.delta)
+      if (length(object$delta) == 1L) {
+         names(ses$delta) <- "delta"
+      } else {
+         names(ses$delta) <- paste0("delta.", seq_along(object$delta))
+      }
+      if (isTRUE(ddd$type=="delta"))
+         return(ses$delta)
+   }
+
+   return(ses)
+
+}
diff --git a/R/zzz.r b/R/zzz.r
@@ -1,6 +1,6 @@
 .onAttach <- function(libname, pkgname) {
 
-   ver <- "4.7-2"
+   ver <- "4.7-3"
 
    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--2-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version)
+[![devel Version](https://img.shields.io/badge/devel-4.7--3-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/_pkgdown.yml b/_pkgdown.yml
@@ -197,6 +197,7 @@ reference:
       - coef.rma
       - coef.permutest.rma.uni
       - vcov.rma
+      - se.rma
       - model.matrix.rma
       - formula.rma
       - coef.matreg

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/articles/pkgdown/diagram.png b/docs/articles/pkgdown/diagram.png
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
@@ -1,9 +1,9 @@
 pandoc: '2.5'
-pkgdown: 2.0.7
+pkgdown: 2.0.8
 pkgdown_sha: ~
 articles:
   diagram: pkgdown/diagram.html
-last_built: 2024-03-28T16:24Z
+last_built: 2024-04-12T16:48Z
 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