Update rerun for osmasem2

Author: mikewlcheung

R/create.mxModel.R

@@ -139,11 +139,14 @@ create.mxModel <- function(model.name="mxModel", RAM=NULL, data=NULL,
   ## Create an identity matrix from the no. of columens of Fmatrix,
   ## including all latent and observed variables
   Id <- as.mxMatrix(diag(ncol(Fmatrix$values)), name="Id")
-
-  ## Expected covariance matrix and means of the observed and latent variables
   Id_A <- mxAlgebra(solve(Id - Amatrix), name="Id_A")
+  
+  ## Note. expCov and expMean are NOT used in the fit function.
+  ## They are included so the implied structures include the latent variables.
+  ## It may be useful for future applications.
   expCov <- mxAlgebra(Id_A %&% Smatrix, name="expCov")   
-    
+  expMean <- mxAlgebra(Mmatrix %*% t(Id_A), name="expMean")
+  
   ## Add the mean structure only if there are means
   if (!is.null(data) | !is.null(means)) {
 
@@ -153,8 +156,7 @@ create.mxModel <- function(model.name="mxModel", RAM=NULL, data=NULL,
       M <- as.mxAlgebra(M, startvalues=startvalues, name="Mmatrix")
       mx.model <- mxModel(mx.model, M$mxalgebra, M$parameters, M$list)
     }
-        
-    expMean <- mxAlgebra(Mmatrix %*% t(Id_A), name="expMean")
+          
     mx.model <- mxModel(mx.model, Fmatrix, Id, Id_A, expCov, expMean,
                         mxCI(c("Amatrix", "Smatrix", "Mmatrix")))
   } else {

R/rerun.R

@@ -2,18 +2,23 @@ rerun <- function(object, autofixtau2=FALSE, extraTries=10, ...) {
   if (!is.element(class(object)[1], c("wls", "tssem1FEM", "tssem1REM", "meta",
                                       "meta3LFIML", "reml",
                                       "tssem1FEM.cluster", "wls.cluster",
-                                      "osmasem", "osmasem3L", "MxModel",
-                                      "mxRAMmodel")))
-    stop("\"object\" must be an object of neither class \"meta\", \"meta3LFIML\", \"wls\", \"reml\", \"tssem1FEM\", \"tssem1REM\", \"tssem1FEM.cluster\", \"wls.cluster\", \"osmasem\", \"osmasem3L\", \"MxModel\", or \"mxRAMModel\".")
+                                      "osmasem", "osmasem2", "osmasem3L",
+                                      "MxModel", "mxRAMmodel")))
+    stop("'object' must be an object of neither class 'meta', 'meta3LFIML',
+'wls', 'reml', 'tssem1FEM', 'tssem1REM', 'tssem1FEM.cluster', 'wls.cluster',
+'osmasem', 'osmasem2', 'osmasem3L', 'MxModel', or 'mxRAMModel'.")
 
   ## Run a rerun without autofixtau2 to minimize over-fixing
   ## Many of the NA in SEs may disappear after rerunning it.
-  if (autofixtau2 & is.element(class(object)[1], c("tssem1REM", "meta", "osmasem"))) {
+  if (autofixtau2 & is.element(class(object)[1], c("tssem1REM", "meta",
+                                                   "osmasem", "osmasem2"))) {
     object <- rerun(object, autofixtau2=FALSE, extraTries=extraTries, ...)
   }
 
   ## Automatically fix the problematic Tau2 into 0 for tssem1REM and meta objects
-  if (autofixtau2 & is.element(class(object)[1], c("tssem1REM", "meta"))) {
+  ## osmasem2 object is similar to meta object as it uses Tau2
+  if (autofixtau2 & is.element(class(object)[1], c("tssem1REM", "meta",
+                                                   "osmasem2"))) {
     ## Get the Tau2 with NA is SE
     tau2nan <- suppressWarnings(sqrt(diag(vcov(object, select="random"))))
 
@@ -78,6 +83,11 @@ rerun <- function(object, autofixtau2=FALSE, extraTries=10, ...) {
                                          bestInitsOutput=FALSE,
                                          intervals=TRUE, ...))
     }
-  }    
+  }
+  ## Run it again as the SEs sometimes diasapper
+  fit <- out$mx.fit
+  fit <- mxOption(fit, "Calculate Hessian", "Yes")
+  fit <- mxOption(fit, "Standard Errors", "Yes")
+  out$mx.fit <- mxRun(fit, silent=TRUE, suppressWarnings=TRUE)
   out
 }