Update create.mxModel

mikewlcheung · Apr 8, 2024 · b279e06 · b279e06
1 parent a4bc650
commit b279e06
Show file tree

Hide file tree

Showing 56 changed files with 789 additions and 503 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: metaSEM
 Type: Package
 Title: Meta-Analysis using Structural Equation Modeling
-Version: 1.3.1
-Date: 2023-08-08
+Version: 1.4.0
+Date: 2024-04-08
 Depends: R (>= 3.4.0), OpenMx
 Imports: Matrix, MASS, ellipse, graphics, stats, utils, mvtnorm, numDeriv, lavaan
 Suggests: metafor, semPlot, R.rsp, testthat, matrixcalc

diff --git a/NAMESPACE b/NAMESPACE
@@ -14,6 +14,7 @@ S3method(plot, meta)
 S3method(plot, character)
 S3method(plot, wls)
 S3method(plot, osmasem)
+S3method(plot, mxRAMmodel)
 # S3method(plot, osmasem3L)
 
 S3method(summary, wls)
@@ -28,6 +29,7 @@ S3method(summary, CorPop)
 S3method(summary, Cor3L)
 S3method(summary, bootuniR2)
 S3method(summary, osmasem)
+S3method(summary, mxRAMmodel)
 # S3method(summary, osmasem3L)
 # S3method(summary, tssemRobust1)
 
@@ -36,6 +38,7 @@ S3method(anova, meta3LFIML)
 S3method(anova, wls)
 S3method(anova, reml)
 S3method(anova, osmasem)
+S3method(anova, mxRAMmodel)
 # S3method(anova, osmasem3L)
 
 S3method(coef, tssem1FEM) 
@@ -46,8 +49,8 @@ S3method(coef, tssem1REM)
 S3method(coef, meta)
 S3method(coef, meta3LFIML)
 S3method(coef, reml)
-S3method(coef, MxRAMModel)
 S3method(coef, osmasem)
+S3method(coef, mxRAMmodel)
 # S3method(coef, osmasem3L)
 # S3method(coef, tssemRobust1)
 
@@ -59,8 +62,8 @@ S3method(vcov, tssem1REM)
 S3method(vcov, meta)
 S3method(vcov, meta3LFIML)
 S3method(vcov, reml)
-S3method(vcov, MxRAMModel)
 S3method(vcov, osmasem)
+S3method(vcov, mxRAMmodel)
 # S3method(vcov, osmasem3L)
 # S3method(vcov, tssemRobust1)
 
@@ -81,6 +84,7 @@ S3method(print, uniR1)
 S3method(print, summary.CorPop)
 S3method(print, summary.Cor3L)
 S3method(print, summary.bootuniR2)
+S3method(print, summary.mxRAMmodel)
 
 # required by R3.3
 importFrom("graphics", "abline", "arrows", "layout", "par", "plot",

diff --git a/NEWS b/NEWS
@@ -1,3 +1,8 @@
+Release 1.4.0 (Apr 8, 2024)
+====================================
+* Revise create.mxModel().
+* Replace dontrun with donttest.
+
 Release 1.3.1 (Aug 8, 2023)
 ====================================
 * Lower the tolerance in testing asyCov(), which returns an error in latest R.

diff --git a/R/as.mxMatrix.R b/R/as.mxMatrix.R
@@ -72,14 +72,16 @@ as.mxMatrix <- function(x, name, ...) {
 }
 
 as.symMatrix <- function(x) {
-    if (is.list(x)) {
-        for (i in seq_along(x)) {
-            x[[i]][] <- vapply(x[[i]], function(z) gsub(".*\\*", "", z), character(1))
-        }
-    } else {
-        x[] <- vapply(x, function(z) gsub(".*\\*", "", z), character(1))
+  if (is.list(x)) {
+    ## for (i in seq_along(x)) {
+    ## Exclude mxalgebras, which creates troubles
+    for (i in c("A", "S", "F", "M")) {
+      x[[i]][] <- vapply(x[[i]], function(z) gsub(".*\\*", "", z), character(1))
     }
-    x
+  } else {
+    x[] <- vapply(x, function(z) gsub(".*\\*", "", z), character(1))
+  }
+  x
 }
 
 as.mxAlgebra <- function(x, startvalues=NULL, name="X") {