Release to CRAN 1.4

mikewlcheung · May 17, 2024 · 8507c3d · 8507c3d
1 parent b279e06
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: metaSEM
 Type: Package
 Title: Meta-Analysis using Structural Equation Modeling
 Version: 1.4.0
-Date: 2024-04-08
+Date: 2024-05-15
 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/NEWS b/NEWS
@@ -1,10 +1,12 @@
-Release 1.4.0 (Apr 8, 2024)
+Release 1.4.0 (May 15, 2024)
 ====================================
+* Release to CRAN.
 * Revise create.mxModel().
 * Replace dontrun with donttest.
 
 Release 1.3.1 (Aug 8, 2023)
 ====================================
+* Release to CRAN.
 * Lower the tolerance in testing asyCov(), which returns an error in latest R.
 
 Release 1.3.0 (Jan 7, 2023)

diff --git a/R/create.mxModel.R b/R/create.mxModel.R
@@ -173,22 +173,25 @@ create.mxModel <- function(model.name="mxModel", RAM=NULL, data=NULL,
     }
   }
 
-  if (run==FALSE) return(mx.model)
+  if (run) {
 
-  ## Default is z
-  mx.fit <- tryCatch(mxRun(mx.model, intervals=(intervals.type=="LB"),
-                           suppressWarnings=TRUE, silent=TRUE, ...),
-                     error=function(e) e)
-
-  ## Check if any errors
-  if (inherits(mx.fit, "error")) {
-    mx.fit <- mxTryHard(mx.model, extraTries=50, intervals=FALSE, silent=TRUE)                        
-    mx.fit <- tryCatch(mxRun(mx.fit, intervals=(intervals.type=="LB"),
+    ## Default is z
+    mx.fit <- tryCatch(mxRun(mx.model, intervals=(intervals.type=="LB"),
                              suppressWarnings=TRUE, silent=TRUE, ...),
                        error=function(e) e)
-    if (inherits(mx.fit, "error")) {   
-      warning("Error in running mxModel.\n")
+
+    ## Check if any errors
+    if (inherits(mx.fit, "error")) {
+      mx.fit <- mxTryHard(mx.model, extraTries=50, intervals=FALSE, silent=TRUE)                        
+      mx.fit <- tryCatch(mxRun(mx.fit, intervals=(intervals.type=="LB"),
+                               suppressWarnings=TRUE, silent=TRUE, ...),
+                         error=function(e) e)
+      if (inherits(mx.fit, "error")) {   
+        warning("Error in running mxModel.\n")
+      }
     }
+  } else {
+    mx.fit <- mx.model
   }
 
   out <- list(mx.fit=mx.fit, RAM=RAM, data=data, mxalgebras=mxalgebras.ci,

diff --git a/R/meta2semPlot.R b/R/meta2semPlot.R
@@ -161,8 +161,8 @@ plot.osmasem <- function(x, manNames=NULL, latNames=NULL, labels=c("labels", "RA
 
   labels <- match.arg(labels)
   if (labels=="labels") {
-      A.labels <- x$mx.model$A0$labels
-      S.labels <- x$mx.model$S0$labels
+      A.labels <- x$mx.fit$A0$labels
+      S.labels <- x$mx.fit$S0$labels
       labels <- c(c(A.labels), c(S.labels))
       row.pars <- as.numeric(row.names(out@Pars))
       out@Pars$label <- labels[row.pars]

diff --git a/R/osmasem.R b/R/osmasem.R
@@ -512,14 +512,13 @@ osmasem <- function(model.name="osmasem", RAM=NULL, Mmatrix=NULL,
     ## Assign same starting values, e.g., A and S matrices are different from those in provided in Jmatrix
     mx.model <- omxAssignFirstParameters(mx.model)
 
-    ## Return mx model without running the analysis
-    if (run==FALSE) {
-        return(mx.model)
-    } else {        
+    if (run) {        
         mx.fit <- tryCatch(do.call(mxRun, c(list(mx.model, intervals=intervals,
                                                  suppressWarnings=suppressWarnings,
                                                  silent=silent),
                                             mxRun.Args)), error = function(e) e)
+    } else {
+        mx.fit <- mx.model
     }
 
     # try to run it with error message as output
@@ -538,7 +537,8 @@ osmasem <- function(model.name="osmasem", RAM=NULL, Mmatrix=NULL,
                 mxRun.Args=mxRun.Args,
                 subset.variables=subset.variables,
                 subset.rows=subset.rows,
-                mx.model=mx.model, mx.fit=mx.fit)
+                #mx.model=mx.model,
+                mx.fit=mx.fit)
     class(out) <- 'osmasem'
     out
 }

diff --git a/man/Cheung09.Rd b/man/Cheung09.Rd
@@ -16,8 +16,6 @@ A list of data with the following structure:
   \item{n}{A vector of sample sizes}
 }
 }
-\source{Cheung, M. W.-L. (2009). TSSEM: A LISREL syntax generator for two-stage structural equation modeling (Version 1.11) [Computer software]. Retrieved from \url{http://courses.nus.edu.sg/course/psycwlm/internet/tssem.zip}.
-}
 \references{
   Cheung, M. W.-L., & Chan, W. (2005). Meta-analytic structural equation modeling: A two-stage approach. \emph{Psychological Methods}, \bold{10}, 40-64.
 

diff --git a/man/metaSEM-package.Rd b/man/metaSEM-package.Rd
@@ -15,7 +15,7 @@
 Package: \tab metaSEM\cr
 Type: \tab Package\cr
 Version: \tab 1.4.0\cr
-Date: \tab 2024-04-08\cr
+Date: \tab 2024-05-15\cr
 License: \tab GPL (>=2)\cr
 LazyLoad: \tab yes\cr
 }

diff --git a/man/tssem1.Rd b/man/tssem1.Rd
@@ -41,8 +41,8 @@ tssem1REM(Cov, n, cor.analysis=TRUE, RE.type=c("Diag", "Symm", "Zero","User"),
   }
   \item{RE.type}{Either \code{"Diag"}, \code{"Symm"},  
 	\code{"Zero"} or \code{"User"}. If it is
-	\code{"Diag"}, a diagonal matrix is used for the random effects
-	meaning that the random effects are independent. If it is \code{"Symm"} (default if missing), a
+	\code{"Diag"} (default if missing), a diagonal matrix is used for the random effects
+	meaning that the random effects are independent. If it is \code{"Symm"}, a
 	symmetric matrix is used for the random effects on the covariances
 	among the correlation (or covariance) vectors. If it is
 	\code{"Zero"}, there is no random effects which is similar to the

diff --git a/vignettes/Examples.html b/vignettes/Examples.html
diff --git a/vignettes/metaSEM.pdf b/vignettes/metaSEM.pdf