Optimizers 'Rcgmin' and 'Rvmmin' available again.

wviechtb · Apr 15, 2024 · 0014f62 · 0014f62
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,11 +1,11 @@
 Package: metafor
-Version: 4.7-3
-Date: 2024-04-12
+Version: 4.7-4
+Date: 2024-04-15
 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
 Imports: stats, utils, graphics, grDevices, nlme, mathjaxr, pbapply
-Suggests: lme4, pracma, minqa, nloptr, dfoptim, ucminf, lbfgsb3c, subplex, BB, Rsolnp, alabama, optimParallel, CompQuadForm, mvtnorm, BiasedUrn, Epi, survival, GLMMadaptive, glmmTMB, multcomp, gsl, sp, ape, boot, clubSandwich, crayon, R.rsp, testthat, rmarkdown, wildmeta, emmeans, estmeansd, metaBLUE, rstudioapi
+Suggests: lme4, pracma, minqa, nloptr, dfoptim, ucminf, lbfgsb3c, subplex, BB, Rsolnp, alabama, optimParallel, optimx, CompQuadForm, mvtnorm, BiasedUrn, Epi, survival, GLMMadaptive, glmmTMB, multcomp, gsl, sp, ape, boot, clubSandwich, crayon, R.rsp, testthat, rmarkdown, wildmeta, emmeans, estmeansd, metaBLUE, rstudioapi
 Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit equal-, fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, bubble, and GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted. An introduction to the package can be found in Viechtbauer (2010) <doi:10.18637/jss.v036.i03>.
 License: GPL (>=2)
 ByteCompile: TRUE

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,6 @@
-# metafor 4.7-3 (2024-04-12)
+# metafor 4.7-4 (2024-04-15)
+
+- made optimizers `Rcgmin` and `Rvmmin` available again via the `optimx` package
 
 - argument `shade` in `funnel()` now automatically uses a color gradient for the regions when multiple `level` values are specified
 

diff --git a/R/misc.func.hidden.r b/R/misc.func.hidden.r
@@ -160,7 +160,7 @@
    if (as.list) {
       return(list(x=x.flip, y=y.flip))
    } else {
-      return(cbind(x.flip, y.flip))
+      return(unname(cbind(x.flip, y.flip)))
    }
 
 }
@@ -1659,14 +1659,9 @@
          stop(mstyle$stop("Please install the 'alabama' package to use this optimizer."), call.=FALSE)
    }
 
-   if (optimizer == "Rcgmin") {
-      if (!requireNamespace(optimizer, quietly=TRUE))
-         stop(mstyle$stop(paste0("Please install the '", optimizer, "' package to use this optimizer.")), call.=FALSE)
-   }
-
-   if (optimizer == "Rvmmin") {
-      if (!requireNamespace(optimizer, quietly=TRUE))
-         stop(mstyle$stop(paste0("Please install the '", optimizer, "' package to use this optimizer.")), call.=FALSE)
+   if (is.element(optimizer, c("Rcgmin","Rvmmin"))) {
+      if (!requireNamespace("optimx", quietly=TRUE))
+         stop(mstyle$stop(paste0("Please install the 'optimx' package to use this optimizer.")), call.=FALSE)
    }
 
    #########################################################################
@@ -1741,16 +1736,16 @@
 
    if (optimizer == "Rcgmin") {
       par.arg <- "par"
-      optimizer <- "Rcgmin::Rcgmin"
-      #ctrl.arg <- ", gr='grnd', control=optcontrol"
-      ctrl.arg <- ", control=optcontrol"
+      optimizer <- "optimx::Rcgmin"
+      ctrl.arg <- ", gr='grnd', control=optcontrol"
+      #ctrl.arg <- ", control=optcontrol"
    }
 
    if (optimizer == "Rvmmin") {
       par.arg <- "par"
-      optimizer <- "Rvmmin::Rvmmin"
-      #ctrl.arg <- ", gr='grnd', control=optcontrol"
-      ctrl.arg <- ", control=optcontrol"
+      optimizer <- "optimx::Rvmmin"
+      ctrl.arg <- ", gr='grnd', control=optcontrol"
+      #ctrl.arg <- ", control=optcontrol"
    }
 
    if (optimizer == "optimParallel") {
@@ -1780,7 +1775,7 @@
    if (optimizer == "lbfgsb3c::lbfgsb3c" && is.null(opt.res$convergence)) # special provision for lbfgsb3c in case 'convergence' is missing
       opt.res$convergence <- -99
 
-   if (is.element(optimizer, c("optim","constrOptim","nlminb","dfoptim::hjk","dfoptim::nmk","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","Rsolnp::solnp","alabama::constrOptim.nl","Rcgmin::Rcgmin","Rvmmin:Rvmmin","optimParallel::optimParallel")) && opt.res$convergence != 0)
+   if (is.element(optimizer, c("optim","constrOptim","nlminb","dfoptim::hjk","dfoptim::nmk","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","Rsolnp::solnp","alabama::constrOptim.nl","optimx::Rcgmin","optimx:Rvmmin","optimParallel::optimParallel")) && opt.res$convergence != 0)
       stop(mstyle$stop(paste0("Optimizer (", optimizer, ") did not achieve convergence (convergence = ", opt.res$convergence, ").")), call.=FALSE)
 
    if (is.element(optimizer, c("dfoptim::mads")) && opt.res$convergence > optcontrol$tol)

diff --git a/R/rma.glmm.r b/R/rma.glmm.r
@@ -833,10 +833,15 @@ test="z", level=95, btt, nAGQ=7, verbose=FALSE, digits, control, ...) {
             stop(mstyle$stop("Please install the 'BB' package to use this optimizer."))
       }
 
+      if (is.element(optimizer, c("Rcgmin","Rvmmin"))) {
+         if (!requireNamespace("optimx", quietly=TRUE))
+            stop(mstyle$stop(paste0("Please install the 'optimx' package to use this optimizer.")))
+      }
+
       if (is.element(optimizer, c("optim","nlminb","uobyqa","newuoa","bobyqa","nloptr","nlm","hjk","nmk","mads","ucminf","lbfgsb3c","subplex","BBoptim","optimParallel","Rcgmin","Rvmmin"))) {
          con$hesspack <- match.arg(con$hesspack, c("numDeriv","pracma"))
          if (!requireNamespace(con$hesspack, quietly=TRUE))
-         stop(mstyle$stop(paste0("Please install the '", con$hesspack, "' package to fit this model.")))
+            stop(mstyle$stop(paste0("Please install the '", con$hesspack, "' package to fit this model.")))
          if (con$dnchgcalc == "dFNCHypergeo") {
             if (!requireNamespace("BiasedUrn", quietly=TRUE))
                stop(mstyle$stop("Please install the 'BiasedUrn' package to fit this model."))
@@ -1643,16 +1648,16 @@ test="z", level=95, btt, nAGQ=7, verbose=FALSE, digits, control, ...) {
 
             if (optimizer == "Rcgmin") {
                par.arg <- "par"
-               optimizer <- "Rcgmin::Rcgmin"
-               #ctrl.arg <- ", gr='grnd', control=optCtrl"
-               ctrl.arg <- ", control=optCtrl"
+               optimizer <- "optimx::Rcgmin"
+               ctrl.arg <- ", gr='grnd', control=optCtrl"
+               #ctrl.arg <- ", control=optCtrl"
             }
 
             if (optimizer == "Rvmmin") {
                par.arg <- "par"
-               optimizer <- "Rvmmin::Rvmmin"
-               #ctrl.arg <- ", gr='grnd', control=optCtrl"
-               ctrl.arg <- ", control=optCtrl"
+               optimizer <- "optimx::Rvmmin"
+               ctrl.arg <- ", gr='grnd', control=optCtrl"
+               #ctrl.arg <- ", control=optCtrl"
             }
 
             if (optimizer == "optimParallel") {
@@ -1727,7 +1732,7 @@ test="z", level=95, btt, nAGQ=7, verbose=FALSE, digits, control, ...) {
 
             ### convergence checks
 
-            if (is.element(optimizer, c("optim","nlminb","dfoptim::hjk","dfoptim::nmk","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","Rcgmin::Rcgmin","Rvmmin:Rvmmin","optimParallel::optimParallel")) && res.FE$convergence != 0)
+            if (is.element(optimizer, c("optim","nlminb","dfoptim::hjk","dfoptim::nmk","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","optimx::Rcgmin","optimx::Rvmmin","optimParallel::optimParallel")) && res.FE$convergence != 0)
                stop(mstyle$stop(paste0("Cannot fit FE model. Optimizer (", optimizer, ") did not achieve convergence (convergence = ", res.FE$convergence, ").")))
 
             if (is.element(optimizer, c("dfoptim::mads")) && res.FE$convergence > optCtrl$tol)
@@ -1766,7 +1771,7 @@ test="z", level=95, btt, nAGQ=7, verbose=FALSE, digits, control, ...) {
 
             ### log-likelihood
 
-            if (is.element(optimizer, c("optim","dfoptim::hjk","dfoptim::nmk","dfoptim::mads","ucminf::ucminf","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","Rcgmin::Rcgmin","Rvmmin:Rvmmin","optimParallel::optimParallel")))
+            if (is.element(optimizer, c("optim","dfoptim::hjk","dfoptim::nmk","dfoptim::mads","ucminf::ucminf","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","optimx::Rcgmin","optimx::Rvmmin","optimParallel::optimParallel")))
                ll.FE <- -1 * res.FE$value
             if (is.element(optimizer, c("nlminb","nloptr::nloptr")))
                ll.FE <- -1 * res.FE$objective
@@ -1822,7 +1827,7 @@ test="z", level=95, btt, nAGQ=7, verbose=FALSE, digits, control, ...) {
 
                   ### convergence checks
 
-                  if (QEconv && is.element(optimizer, c("optim","nlminb","dfoptim::hjk","dfoptim::nmk","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","Rcgmin::Rcgmin","Rvmmin:Rvmmin","optimParallel::optimParallel")) && res.QE$convergence != 0) {
+                  if (QEconv && is.element(optimizer, c("optim","nlminb","dfoptim::hjk","dfoptim::nmk","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","optimx::Rcgmin","optimx:Rvmmin","optimParallel::optimParallel")) && res.QE$convergence != 0) {
                      warning(mstyle$warning(paste0("Cannot fit saturated model. Optimizer (", optimizer, ") did not achieve convergence (convergence = ", res.QE$convergence, ").")), call.=FALSE)
                      QEconv <- FALSE
                      ll.QE <- NA_real_
@@ -1887,7 +1892,7 @@ test="z", level=95, btt, nAGQ=7, verbose=FALSE, digits, control, ...) {
 
                ### log-likelihood
 
-               if (is.element(optimizer, c("optim","dfoptim::hjk","dfoptim::nmk","dfoptim::mads","ucminf::ucminf","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","Rcgmin::Rcgmin","Rvmmin:Rvmmin","optimParallel::optimParallel")))
+               if (is.element(optimizer, c("optim","dfoptim::hjk","dfoptim::nmk","dfoptim::mads","ucminf::ucminf","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","optimx::Rcgmin","optimx::Rvmmin","optimParallel::optimParallel")))
                   ll.QE <- -1 * res.QE$value
                if (is.element(optimizer, c("nlminb","nloptr::nloptr")))
                   ll.QE <- -1 * res.QE$objective
@@ -2067,7 +2072,7 @@ test="z", level=95, btt, nAGQ=7, verbose=FALSE, digits, control, ...) {
 
             ### convergence checks
 
-            if (is.element(optimizer, c("optim","nlminb","dfoptim::hjk","dfoptim::nmk","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","Rcgmin::Rcgmin","Rvmmin:Rvmmin","optimParallel::optimParallel")) && res.ML$convergence != 0)
+            if (is.element(optimizer, c("optim","nlminb","dfoptim::hjk","dfoptim::nmk","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","optimx::Rcgmin","optimx::Rvmmin","optimParallel::optimParallel")) && res.ML$convergence != 0)
                stop(mstyle$stop(paste0("Cannot fit ML model. Optimizer (", optimizer, ") did not achieve convergence (convergence = ", res.ML$convergence, ").")))
 
             if (is.element(optimizer, c("dfoptim::mads")) && res.ML$convergence > optCtrl$tol)
@@ -2111,7 +2116,7 @@ test="z", level=95, btt, nAGQ=7, verbose=FALSE, digits, control, ...) {
 
             ### log-likelihood
 
-            if (is.element(optimizer, c("optim","dfoptim::hjk","dfoptim::nmk","dfoptim::mads","ucminf::ucminf","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","Rcgmin::Rcgmin","Rvmmin:Rvmmin","optimParallel::optimParallel")))
+            if (is.element(optimizer, c("optim","dfoptim::hjk","dfoptim::nmk","dfoptim::mads","ucminf::ucminf","lbfgsb3c::lbfgsb3c","subplex::subplex","BB::BBoptim","optimx::Rcgmin","optimx:Rvmmin","optimParallel::optimParallel")))
                ll.ML <- -1 * res.ML$value
             if (is.element(optimizer, c("nlminb","nloptr::nloptr")))
                ll.ML <- -1 * res.ML$objective

diff --git a/R/selmodel.rma.uni.r b/R/selmodel.rma.uni.r
@@ -222,7 +222,7 @@ selmodel.rma.uni <- function(x, type, alternative="greater", prec, delta, steps,
                tau2tol = min(vi/10, 1e-04), # threshold for treating tau^2 as effectively equal to 0 in the Hessian computation
                deltatol = 1e-04,      # threshold for treating deltas as effectively equal to 0 in the Hessian computation (only for stepfun)
                pval.min = NULL,       # minimum p-value to intergrate over (for selection models where this matters)
-               optimizer = "optim",   # optimizer to use ("optim","nlminb","uobyqa","newuoa","bobyqa","nloptr","nlm","hjk","nmk","mads","ucminf","lbfgsb3c","subplex","BBoptim","optimParallel","solnp","alabama"/"constrOptim.nl")
+               optimizer = "optim",   # optimizer to use ("optim","nlminb","uobyqa","newuoa","bobyqa","nloptr","nlm","hjk","nmk","mads","ucminf","lbfgsb3c","subplex","BBoptim","optimParallel","solnp","alabama"/"constrOptim.nl","Rcgmin","Rvmmin")
                optmethod = "BFGS",    # argument 'method' for optim() ("Nelder-Mead" and "BFGS" are sensible options)
                parallel = list(),     # parallel argument for optimParallel() (note: 'cl' argument in parallel is not passed; this is directly specified via 'cl')
                cl = NULL,             # arguments for optimParallel()

diff --git a/R/zzz.r b/R/zzz.r
@@ -1,6 +1,6 @@
 .onAttach <- function(libname, pkgname) {
 
-   ver <- "4.7-3"
+   ver <- "4.7-4"
 
    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--3-brightgreen.svg)](https://www.metafor-project.org/doku.php/installation#development_version)
+[![devel Version](https://img.shields.io/badge/devel-4.7--4-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)
 

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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
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