Allow 'constrOptim' optimizer in location-scale models fitted with rm…

…a() when using an identity link and 'optbeta=TRUE'.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: metafor
-Version: 4.7-1
-Date: 2024-04-09
+Version: 4.7-2
+Date: 2024-04-10
 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

NEWS.md

@@ -1,4 +1,4 @@
-# metafor 4.7-1 (2024-04-09)
+# metafor 4.7-2 (2024-04-10)
 
 - argument `shade` in `funnel()` now automatically uses a color gradient for the regions when multiple `level` values are specified
 

R/rma.uni.r

@@ -1746,26 +1746,15 @@ test="z", level=95, btt, att, tau2, verbose=FALSE, digits, control, ...) {
       if (optimizer == "alabama")
          optimizer <- "constrOptim.nl"
 
-      ### when using an identity link, automatically set 'constrOptim' as the default optimizer (but 'solnp' by default when optbeta=TRUE)
+      ### when using an identity link, automatically set 'constrOptim' as the default optimizer
 
       if (link == "identity") {
-         if (optbeta) {
-            if (optimizer == "nlminb") {
-               optimizer <- "solnp"
-            } else {
-               if (!is.element(optimizer, c("solnp","nloptr","constrOptim.nl"))) {
-                  optimizer <- "solnp"
-                  warning(mstyle$warning(paste0("Can only use optimizers 'solnp', 'nloptr', or 'constrOptim.nl' when link='identity' and optbeta=TRUE (resetting to '", optimizer, "').")), call.=FALSE)
-               }
-            }
+         if (optimizer == "nlminb") {
+            optimizer <- "constrOptim"
          } else {
-            if (optimizer == "nlminb") {
+            if (!is.element(optimizer, c("constrOptim","solnp","nloptr","constrOptim.nl"))) {
                optimizer <- "constrOptim"
-            } else {
-               if (!is.element(optimizer, c("constrOptim","solnp","nloptr","constrOptim.nl"))) {
-                  optimizer <- "constrOptim"
-                  warning(mstyle$warning(paste0("Can only use optimizers 'constrOptim', 'solnp', 'nloptr', or 'constrOptim.nl' when link='identity' (resetting to '", optimizer, "').")), call.=FALSE)
-               }
+               warning(mstyle$warning(paste0("Can only use optimizers 'constrOptim', 'solnp', 'nloptr', or 'constrOptim.nl' when link='identity' (resetting to '", optimizer, "').")), call.=FALSE)
             }
          }
       }
@@ -1842,6 +1831,15 @@ test="z", level=95, btt, att, tau2, verbose=FALSE, digits, control, ...) {
                stop(mstyle$stop(paste0("Length of 'beta' argument (", length(beta), ") does not match actual number of parameters (", p, ").")))
          }
 
+         ### needed for constrOptim() when optbeta=TRUE
+
+         X0 <- X
+         X0[] <- 0
+
+      } else {
+
+         X0 <- NULL
+
       }
 
       ### rescale Z matrix (only for models with moderators, models including a non-fixed intercept term, when not placing constraints on alpha, and when not optimizing over beta)
@@ -2042,7 +2040,7 @@ test="z", level=95, btt, att, tau2, verbose=FALSE, digits, control, ...) {
       if (link == "identity") {
 
          if (optimizer == "constrOptim")
-            optcall <- paste0("constrOptim(theta=c(beta.init, alpha.init), f=.ll.rma.ls, grad=NULL, ui=Z, ci=rep(0,k),
+            optcall <- paste0("constrOptim(theta=c(beta.init, alpha.init), f=.ll.rma.ls, grad=NULL, ui=cbind(X0,Z), ci=rep(0,k),
                               yi=yi, vi=vi, X=X, Z=Z, reml=reml, k=k, pX=p, alpha.arg=alpha, beta.arg=beta, verbose=verbose, digits=digits,
                               REMLf=con$REMLf, link=link, mZ=mZ, alpha.min=alpha.min, alpha.max=alpha.max, alpha.transf=TRUE,
                               tau2.min=con$tau2.min, tau2.max=con$tau2.max, optbeta=optbeta", ctrl.arg, ")\n")

R/zzz.r

@@ -1,6 +1,6 @@
 .onAttach <- function(libname, pkgname) {
 
-   ver <- "4.7-1"
+   ver <- "4.7-2"
 
    loadmsg <- paste0("\nLoading the 'metafor' package (version ", ver, "). For an\nintroduction to the package please type: help(metafor)\n")
 

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--1-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version)
+[![devel Version](https://img.shields.io/badge/devel-4.7--2-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)
 

tests/testthat/test_misc_rma_mv.r

@@ -133,10 +133,13 @@ test_that("rma.mv() correctly handles 'beta' argument", {
    dat <- escalc(measure="RR", ai=tpos, bi=tneg, ci=cpos, di=cneg, data=dat.bcg)
    res <- rma(yi, vi, scale = ~ 1, data=dat, optbeta=TRUE, beta=0)
    ll1 <- logLik(res)
-   res <- rma.mv(yi, vi, random = ~ 1 | trial, data=dat, beta=0)
+   res <- rma(yi, vi, scale = ~ 1, data=dat, optbeta=TRUE, beta=0, link="identity")
    ll2 <- logLik(res)
+   res <- rma.mv(yi, vi, random = ~ 1 | trial, data=dat, beta=0)
+   ll3 <- logLik(res)
 
    expect_equivalent(ll1, ll2, tolerance=.tol[["fit"]])
+   expect_equivalent(ll1, ll3, tolerance=.tol[["fit"]])
 
 })