Rename create.mxModel to sem

DESCRIPTION

@@ -2,7 +2,7 @@ Package: metaSEM
 Type: Package
 Title: Meta-Analysis using Structural Equation Modeling
 Version: 1.4.5
-Date: 2024-07-27
+Date: 2024-08-01
 Depends: R (>= 3.4.0), OpenMx
 Imports: Matrix, MASS, ellipse, graphics, stats, utils, mvtnorm, numDeriv, lavaan
 Suggests: metafor, semPlot, R.rsp, testthat, matrixcalc

NAMESPACE

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

NEWS

@@ -1,3 +1,7 @@
+Release 1.4.5 (Aug 1, 2024)
+====================================
+Rename create.mxModel() to sum().
+
 Release 1.4.4 (Jul 27, 2024)
 ====================================
 * Add osmasem2() and friends.

R/rerun.R

@@ -3,7 +3,7 @@ rerun <- function(object, autofixtau2=FALSE, extraTries=10, ...) {
  "meta3LFIML", "reml",
  "tssem1FEM.cluster", "wls.cluster",
  "osmasem", "osmasem2", "osmasem3L",
- "MxModel", "mxRAMmodel")))
+ "MxModel", "sem")))
  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'.")

R/create.mxModel.R → R/sem.R

@@ -2,11 +2,10 @@
 ## intervals.type="LB", it returns an error because some parameters are
 ## replaced with the new parameters in the constraints. However, the
 ## names of these new parameters are not in the CI object.
-create.mxModel <- function(model.name="mxModel", RAM=NULL, data=NULL,
- Cov=NULL, means=NULL, numObs,
- intervals.type=c("z", "LB"), startvalues=NULL,
- replace.constraints=FALSE, mxModel.Args=NULL,
- run=TRUE, silent=TRUE, ...) {
+sem <- function(model.name="sem", RAM=NULL, data=NULL, Cov=NULL,
+ means=NULL, numObs, intervals.type=c("z", "LB"),
+ startvalues=NULL, replace.constraints=FALSE,
+ mxModel.Args=NULL, run=TRUE, silent=TRUE, ...) {
 
  intervals.type <- match.arg(intervals.type)
 
@@ -21,7 +20,6 @@ create.mxModel <- function(model.name="mxModel", RAM=NULL, data=NULL,
  ## Extract all observed and latent variable names
  var.names <- colnames(Fmatrix$values)
 
-
  ## Without raw data
  if (is.null(data)) {
  ## Without means
@@ -218,13 +216,27 @@ create.mxModel <- function(model.name="mxModel", RAM=NULL, data=NULL,
 
  out <- list(mx.fit=mx.fit, RAM=RAM, data=data, mxalgebras=mxalgebras.ci,
  intervals.type=intervals.type)
- class(out) <- "mxRAMmodel"
+ class(out) <- "sem"
  out
 }
 
-summary.mxRAMmodel <- function(object, robust=FALSE, ...) {
- if (!is.element("mxRAMmodel", class(object)))
- stop("\"object\" must be an object of class \"mxRAMmodel\".")
+## Will be depreciated in the future
+create.mxModel <- function(model.name="sem", RAM=NULL, data=NULL,
+ Cov=NULL, means=NULL, numObs,
+ intervals.type=c("z", "LB"), startvalues=NULL,
+ replace.constraints=FALSE, mxModel.Args=NULL,
+ run=TRUE, silent=TRUE, ...) {
+ .Deprecated("create.mxModel")
+ 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\".")
 
  # calculate coefficients 
  my.mx <- summary(object$mx.fit)
@@ -308,13 +320,13 @@ summary.mxRAMmodel <- function(object, robust=FALSE, ...) {
  Minus2LL=my.mx$Minus2LogLikelihood,
  Mx.status1=object$mx.fit@output$status[[1]],
  informationCriteria=informationCriteria)
- class(out) <- "summary.mxRAMmodel"
+ class(out) <- "summary.sem"
  out
 }
 
-print.summary.mxRAMmodel <- function(x, ...) {
- if (!is.element("summary.mxRAMmodel", class(x))) {
- stop("\"x\" must be an object of class \"summary.mxRAMmodel\".")
+print.summary.sem <- function(x, ...) {
+ if (!is.element("summary.sem", class(x))) {
+ stop("\"x\" must be an object of class \"summary.sem\".")
  }
 
  cat("95% confidence intervals: ")
@@ -343,16 +355,16 @@ print.summary.mxRAMmodel <- 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.mxRAMmodel <- function(object, ...) {
- if (!is.element("mxRAMmodel", class(object)))
- stop("\"object\" must be an object of class \"mxRAMmodel\".")
+coef.sem <- function(object, ...) {
+ if (!is.element("sem", class(object)))
+ stop("\"object\" must be an object of class \"sem\".")
 
  coef(object$mx.fit)
 }
 
-vcov.mxRAMmodel <- function(object, robust=FALSE, ...) {
- if (!is.element("mxRAMmodel", class(object)))
- stop("\"object\" must be an object of class \"mxRAMmodel\".")
+vcov.sem <- function(object, robust=FALSE, ...) {
+ if (!is.element("sem", class(object)))
+ stop("\"object\" must be an object of class \"sem\".")
 
  if (robust) {
  suppressMessages(imxRobustSE(object$mx.fit, details=TRUE)$cov)
@@ -361,24 +373,24 @@ vcov.mxRAMmodel <- function(object, robust=FALSE, ...) {
  } 
 }
 
-anova.mxRAMmodel <- function(object, ..., all=FALSE) {
+anova.sem <- 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.mxRAMmodel <- 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.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, ...) {
+ 
  if (!requireNamespace("semPlot", quietly=TRUE)) 
  stop("\"semPlot\" package is required for this function.")
 
- if (!inherits(x, "mxRAMmodel"))
- stop("'mxRAMmodel' object is required.\n")
+ if (!inherits(x, "sem"))
+ stop("'sem' 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.mxRAMmodel}
+\alias{anova.sem}
 \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}{mxRAMmodel}(object, \dots, all=FALSE)
+\method{anova}{sem}(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.mxRAMmodel}
+\alias{coef.sem}
 
 \title{Extract Parameter Estimates from various classes.
 }
@@ -27,14 +27,14 @@
 \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}{mxRAMmodel}(object, \dots)
+\method{coef}{sem}(object, \dots)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{
  \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{reml}, class \code{osmasem}, class \code{osmasem2}, or class \code{mxRAMmodel}
+ \code{reml}, class \code{osmasem}, class \code{osmasem2}, or class \code{sem}
  }
  \item{select}{Select \code{all} for both fixed- and random-effects parameters, \code{fixed} for the
  fixed-effects parameters or \code{random} for the random-effects
@@ -43,7 +43,7 @@
 } 
  \item{\dots}{Further arguments; currently none is used}
 }
-\note{\code{coef.mxRAMmodel} is simply a wraper of
+\note{\code{coef.sem} is simply a wraper of
  \code{omxGetParameters}. Extra arguments will be passed to it}
 
 \value{Parameter estimates for both fixed-effects (if any) and random-effects (if any)

man/metaSEM-package.Rd

@@ -15,7 +15,7 @@
 Package: \tab metaSEM\cr
 Type: \tab Package\cr
 Version: \tab 1.4.5\cr
-Date: \tab 2024-07-27\cr
+Date: \tab 2024-08-01\cr
 License: \tab GPL (>=2)\cr
 LazyLoad: \tab yes\cr
 }

man/plot.Rd

@@ -4,7 +4,7 @@
 \alias{plot.wls}
 \alias{plot.osmasem}
 \alias{plot.osmasem2}
-\alias{plot.mxRAMmodel}
+\alias{plot.sem}
 
 \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}{mxRAMmodel}(x, manNames=NULL, latNames=NULL, labels=c("labels", "RAM"),
+\method{plot}{sem}(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/create.mxModel.Rd → man/sem.Rd

@@ -1,15 +1,22 @@
-\name{create.mxModel}
+\name{sem}
+\alias{sem}
 \alias{create.mxModel}
-\title{Create an mxModel
+\title{Fit a structural equation model using OpenMx
 }
-\description{It creates a mxModel from a RAM object. 
+\description{It fits a structural equation model by creating a mxModel from a RAM object. 
 }
 \usage{
-create.mxModel(model.name="mxModel", RAM=NULL, data=NULL,
+## Depreciated in the future
+create.mxModel(model.name="sem", RAM=NULL, data=NULL,
  Cov=NULL, means=NULL, numObs,
  intervals.type=c("z", "LB"), startvalues=NULL,
  replace.constraints=FALSE, mxModel.Args=NULL,
  run=TRUE, silent=TRUE, ...)
+sem(model.name="sem", RAM=NULL, data=NULL,
+ Cov=NULL, means=NULL, numObs,
+ intervals.type=c("z", "LB"), startvalues=NULL,
+ replace.constraints=FALSE, mxModel.Args=NULL,
+ run=TRUE, silent=TRUE, ...)
 }
 \arguments{
  \item{model.name}{A string for the model name in \code{\link[OpenMx]{mxModel}}. 
@@ -58,7 +65,7 @@ plot(model)
 
 RAM <- lavaan2RAM(model, obs.variables=c("y", "x"))
 
-my.fit <- create.mxModel(RAM=RAM, data=my.df)
+my.fit <- sem(RAM=RAM, data=my.df)
 summary(my.fit)
 
 ## A meta-analysis
@@ -72,7 +79,7 @@ plot(model)
 RAM <- lavaan2RAM(model, obs.variables="yi", std.lv=FALSE)
 
 ## Use likelihood-based CI 
-my.fit <- create.mxModel(RAM=RAM, data=Hox02, intervals="LB")
+my.fit <- sem(RAM=RAM, data=Hox02, intervals="LB")
 summary(my.fit)
 }
 }

man/summary.Rd

@@ -12,7 +12,7 @@
 \alias{summary.bootuniR2}
 \alias{summary.osmasem}
 \alias{summary.osmasem2}
-\alias{summary.mxRAMmodel}
+\alias{summary.sem}
 \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.mxRAMmodel}
+\alias{print.summary.sem}
 \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}{mxRAMmodel}(object, robust=FALSE, \dots)
+\method{summary}{sem}(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}{mxRAMmodel}(x, \dots)
+\method{print.summary}{sem}(x, \dots)
 \method{print.summary}{CorPop}(x, \dots)
 \method{print.summary}{Cor3L}(x, \dots)
 \method{print.summary}{bootuniR2}(x, \dots)

man/vcov.Rd

@@ -9,7 +9,7 @@
 \alias{vcov.reml}
 \alias{vcov.osmasem}
 \alias{vcov.osmasem2}
-\alias{vcov.mxRAMmodel}
+\alias{vcov.sem}
 \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}{mxRAMmodel}(object, robust=FALSE, \dots)
+\method{vcov}{sem}(object, robust=FALSE, \dots)
 }
 %- maybe also 'usage' for other objects documented here.
 \arguments{