Update rerun for osmasem2

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
 }