Change class sem to mxsem as it conflicts with sem package

Author: mikewlcheung

NAMESPACE

@@ -15,7 +15,7 @@ S3method(plot, character)
 S3method(plot, wls)
 S3method(plot, osmasem)
 S3method(plot, osmasem2)
-S3method(plot, sem)
+S3method(plot, mxsem)
 # S3method(plot, osmasem3L)
 
 S3method(summary, wls)
@@ -31,7 +31,7 @@ S3method(summary, Cor3L)
 S3method(summary, bootuniR2)
 S3method(summary, osmasem)
 S3method(summary, osmasem2)
-S3method(summary, sem)
+S3method(summary, mxsem)
 # S3method(summary, osmasem3L)
 # S3method(summary, tssemRobust1)
 
@@ -41,7 +41,7 @@ S3method(anova, wls)
 S3method(anova, reml)
 S3method(anova, osmasem)
 S3method(anova, osmasem2)
-S3method(anova, sem)
+S3method(anova, mxsem)
 # S3method(anova, osmasem3L)
 
 S3method(coef, tssem1FEM) 
@@ -54,7 +54,7 @@ S3method(coef, meta3LFIML)
 S3method(coef, reml)
 S3method(coef, osmasem)
 S3method(coef, osmasem2)
-S3method(coef, sem)
+S3method(coef, mxsem)
 # S3method(coef, osmasem3L)
 # S3method(coef, tssemRobust1)
 
@@ -68,7 +68,7 @@ S3method(vcov, meta3LFIML)
 S3method(vcov, reml)
 S3method(vcov, osmasem)
 S3method(vcov, osmasem2)
-S3method(vcov, sem)
+S3method(vcov, mxsem)
 # S3method(vcov, osmasem3L)
 # S3method(vcov, tssemRobust1)
 
@@ -89,7 +89,7 @@ S3method(print, uniR1)
 S3method(print, summary.CorPop)
 S3method(print, summary.Cor3L)
 S3method(print, summary.bootuniR2)
-S3method(print, summary.sem)
+S3method(print, summary.mxsem)
 
 # required by R3.3
 importFrom("graphics", "abline", "arrows", "layout", "par", "plot",

R/sem.R

@@ -225,7 +225,7 @@ sem <- function(model.name="sem", RAM=NULL, data=NULL, Cov=NULL,
 
   out <- list(mx.fit=mx.fit, RAM=RAM, data=data, mxalgebras=mxalgebras.ci,
               intervals.type=intervals.type)
-  class(out) <- "sem"
+  class(out) <- "mxsem"
   out
 }
 
@@ -235,17 +235,17 @@ create.mxModel <- function(model.name="sem", RAM=NULL, data=NULL,
                            intervals.type=c("z", "LB"), startvalues=NULL,
                            replace.constraints=FALSE, mxModel.Args=NULL,
                            run=TRUE, silent=TRUE, ...) {
-  .Deprecated("create.mxModel")
+  .Deprecated("sem")
   sem(model.name=model.name, RAM=RAM, data=data, Cov=Cov, means=means,
       numObs=numObs, intervals.type=intervals.type, startvalues=startvalues,
       replace.constraints=replace.constraints, mxModel.Args=mxModel.Args,
       run=run, silent=silent, ...)
 }
 
 
-summary.sem <- function(object, robust=FALSE, ...) {
-  if (!is.element("sem", class(object)))
-    stop("\"object\" must be an object of class \"sem\".")
+summary.mxsem <- function(object, robust=FALSE, ...) {
+  if (!is.element("mxsem", class(object)))
+    stop("\"object\" must be an object of class \"mxsem\".")
 
   # calculate coefficients    
   my.mx <- summary(object$mx.fit)
@@ -329,13 +329,13 @@ summary.sem <- function(object, robust=FALSE, ...) {
               Minus2LL=my.mx$Minus2LogLikelihood,
               Mx.status1=object$mx.fit@output$status[[1]],
               informationCriteria=informationCriteria)
-    class(out) <- "summary.sem"
+    class(out) <- "summary.mxsem"
     out
 }
 
-print.summary.sem <- function(x, ...) {
-    if (!is.element("summary.sem", class(x))) {
-      stop("\"x\" must be an object of class \"summary.sem\".")
+print.summary.mxsem <- function(x, ...) {
+    if (!is.element("summary.mxsem", class(x))) {
+      stop("\"x\" must be an object of class \"summary.mxsem\".")
     }
 
     cat("95% confidence intervals: ")
@@ -364,16 +364,15 @@ print.summary.sem <- function(x, ...) {
     if (!(x$Mx.status1 %in% c(0,1))) warning("OpenMx status1 is neither 0 or 1. You are advised to 'rerun' it again.\n")
 }
 
-coef.sem <- function(object, ...) {
-  if (!is.element("sem", class(object)))
-    stop("\"object\" must be an object of class \"sem\".")
-
+coef.mxsem <- function(object, ...) {
+  if (!is.element("mxsem", class(object)))
+    stop("\"object\" must be an object of class \"mxsem\".")
   coef(object$mx.fit)
 }
 
-vcov.sem <- function(object, robust=FALSE, ...) {
-  if (!is.element("sem", class(object)))
-    stop("\"object\" must be an object of class \"sem\".")
+vcov.mxsem <- function(object, robust=FALSE, ...) {
+  if (!is.element("mxsem", class(object)))
+    stop("\"object\" must be an object of class \"mxsem\".")
 
   if (robust) {
     suppressMessages(imxRobustSE(object$mx.fit, details=TRUE)$cov)
@@ -382,24 +381,24 @@ vcov.sem <- function(object, robust=FALSE, ...) {
   } 
 }
 
-anova.sem <- function(object, ..., all=FALSE) {
+anova.mxsem <- function(object, ..., all=FALSE) {
   base <- lapply(list(object), function(x) x$mx.fit)
   comparison <- lapply(list(...), function(x) x$mx.fit)
   mxCompare(base=base, comparison=comparison, all=all)
 }
 
-plot.sem <- function(x, manNames=NULL, latNames=NULL,
-                     labels=c("labels", "RAM"), what="est", nCharNodes=0,
-                     nCharEdges=0, layout=c("tree", "circle", "spring",
-                                            "tree2", "circle2"),
-                     sizeMan=8, sizeLat=8, edge.label.cex=1.3,
-                     color="white", weighted=FALSE, ...) {
+plot.mxsem <- function(x, manNames=NULL, latNames=NULL,
+                       labels=c("labels", "RAM"), what="est", nCharNodes=0,
+                       nCharEdges=0, layout=c("tree", "circle", "spring",
+                                              "tree2", "circle2"),
+                       sizeMan=8, sizeLat=8, edge.label.cex=1.3,
+                       color="white", weighted=FALSE, ...) {
 
   if (!requireNamespace("semPlot", quietly=TRUE))    
     stop("\"semPlot\" package is required for this function.")
 
-  if (!inherits(x, "sem"))
-    stop("'sem' object is required.\n")
+  if (!inherits(x, "mxsem"))
+    stop("'mxsem' object is required.\n")
 
   A <- x$mx.fit@matrices$Amatrix$values
   S <- x$mx.fit@matrices$Smatrix$values

man/anova.Rd

@@ -5,7 +5,7 @@
 \alias{anova.reml}
 \alias{anova.osmasem}
 \alias{anova.osmasem2}
-\alias{anova.sem}
+\alias{anova.mxsem}
 \title{Compare Nested Models with Likelihood Ratio Statistic
 }
 \description{It compares nested models with the likelihood ratio
@@ -18,7 +18,7 @@
 \method{anova}{reml}(object, \dots, all=FALSE)
 \method{anova}{osmasem}(object, \dots, all=FALSE)
 \method{anova}{osmasem2}(object, \dots, all=FALSE)
-\method{anova}{sem}(object, \dots, all=FALSE)
+\method{anova}{mxsem}(object, \dots, all=FALSE)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

man/coef.Rd

@@ -9,7 +9,7 @@
 \alias{coef.reml}
 \alias{coef.osmasem}
 \alias{coef.osmasem2}
-\alias{coef.sem}
+\alias{coef.mxsem}
 
 \title{Extract Parameter Estimates from various classes.
 }
@@ -27,7 +27,7 @@
 \method{coef}{reml}(object, \dots)
 \method{coef}{osmasem}(object, select=c("fixed", "all", "random"), \dots)
 \method{coef}{osmasem2}(object, select=c("fixed", "all", "random"), \dots)
-\method{coef}{sem}(object, \dots)
+\method{coef}{mxsem}(object, \dots)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{

man/plot.Rd

@@ -4,7 +4,7 @@
 \alias{plot.wls}
 \alias{plot.osmasem}
 \alias{plot.osmasem2}
-\alias{plot.sem}
+\alias{plot.mxsem}
 
 \title{Plot methods for various objects
 }
@@ -48,7 +48,7 @@
      layout=c("tree", "circle", "spring", "tree2", "circle2"),
      sizeMan=8, sizeLat=8, edge.label.cex=1.3, color="white",
   weighted=FALSE, \dots)
-\method{plot}{sem}(x, manNames=NULL, latNames=NULL, labels=c("labels", "RAM"),
+\method{plot}{mxsem}(x, manNames=NULL, latNames=NULL, labels=c("labels", "RAM"),
      what="est", nCharNodes=0, nCharEdges=0,
      layout=c("tree", "circle", "spring", "tree2", "circle2"),
      sizeMan=8, sizeLat=8, edge.label.cex=1.3, color="white",

man/sem.Rd

@@ -46,7 +46,7 @@ sem(model.name="sem", RAM=NULL, data=NULL,
 \item{\dots}{Further arguments will be passed to either
   \code{\link[OpenMx]{mxRun}} or \code{\link[OpenMx]{mxTryHard}}}  
 }
-\value{An object of class \code{mxRAMmodel}}
+\value{An object of class \code{mxsem}}
 \note{when there are constraints with \code{replace.constraints=TRUE} and \code{intervals.type="LB"}, it returns an error because some parameters in the model are replaced with the new parameters in the constraints. However, the names of these new parameters are not captured in the CI object. Users are advised to use \code{intervals.type="z"} before it is fixed.
 }
 \author{Mike W.-L. Cheung <mikewlcheung@nus.edu.sg>

man/summary.Rd

@@ -12,7 +12,7 @@
 \alias{summary.bootuniR2}
 \alias{summary.osmasem}
 \alias{summary.osmasem2}
-\alias{summary.sem}
+\alias{summary.mxsem}
 \alias{print.summary.tssem1FEM}
 \alias{print.summary.tssem1FEM.cluster}
 \alias{print.summary.wls}
@@ -22,7 +22,7 @@
 \alias{print.summary.CorPop}
 \alias{print.summary.Cor3L}
 \alias{print.summary.bootuniR2}
-\alias{print.summary.sem}
+\alias{print.summary.mxsem}
 \title{Summary Method for tssem1, wls, meta, and meta3LFIML Objects
 }
 \description{It summaries results for various class.
@@ -36,7 +36,7 @@
 \method{summary}{meta}(object, homoStat=TRUE, robust=FALSE, \dots)
 \method{summary}{meta3LFIML}(object, allX=FALSE, robust=FALSE, \dots)
 \method{summary}{reml}(object, \dots)
-\method{summary}{sem}(object, robust=FALSE, \dots)
+\method{summary}{mxsem}(object, robust=FALSE, \dots)
 \method{summary}{CorPop}(object, \dots)
 \method{summary}{Cor3L}(object, \dots)
 \method{summary}{bootuniR2}(object, probs=c(0, 0.1, 0.5, 0.9, 1),
@@ -49,7 +49,7 @@
 \method{print.summary}{meta}(x, \dots)
 \method{print.summary}{meta3LFIML}(x, \dots)
 \method{print.summary}{reml}(x, \dots)
-\method{print.summary}{sem}(x, \dots)
+\method{print.summary}{mxsem}(x, \dots)
 \method{print.summary}{CorPop}(x, \dots)
 \method{print.summary}{Cor3L}(x, \dots)
 \method{print.summary}{bootuniR2}(x, \dots)
@@ -58,7 +58,7 @@
   \item{object}{An object returned from either class
 	\code{tssem1FEM}, class \code{tssem1FEM.cluster},
 	class \code{tssem1REM}, class \code{wls}, class \code{wls.cluster},
-	class \code{meta}, class \code{meta3LFIML}, class \code{reml} or class \code{CorPop}.
+	class \code{meta}, class \code{meta3LFIML}, class \code{reml}, class \code{mxsem} or class \code{CorPop}.
 }
   \item{x}{An object returned from either class \code{summary.tssem1FEM},
 	class \code{tssem1FEM.cluster}, class \code{summary.wls}, class

man/vcov.Rd

@@ -9,7 +9,7 @@
 \alias{vcov.reml}
 \alias{vcov.osmasem}
 \alias{vcov.osmasem2}
-\alias{vcov.sem}
+\alias{vcov.mxsem}
 \title{Extract Covariance Matrix Parameter Estimates from Objects of
   Various Classes
 }
@@ -27,7 +27,7 @@
 \method{vcov}{reml}(object, \dots)
 \method{vcov}{osmasem}(object, select=c("fixed", "all", "random"), robust=FALSE, \dots)
 \method{vcov}{osmasem2}(object, select=c("fixed", "all", "random"), robust=FALSE, \dots)
-\method{vcov}{sem}(object, robust=FALSE, \dots)
+\method{vcov}{mxsem}(object, robust=FALSE, \dots)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{