Cleanup namespace of extract functions, reduce references to these fu…

…nctions in documentation

DESCRIPTION

@@ -51,6 +51,6 @@ Suggests:
 LazyLoad: yes
 LazyData: yes
 VignetteBuilder: knitr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Encoding: UTF-8
 Config/testthat/edition: 3

NAMESPACE

@@ -24,12 +24,6 @@ export(detectMplus)
 export(detectVariables)
 export(extract.mplus.model)
 export(extract.mplusObject)
-export(extractModIndices)
-export(extractModelParameters)
-export(extractModelSummaries)
-export(getSavedata_Bparams)
-export(getSavedata_Data)
-export(getSavedata_Fileinfo)
 export(get_bparameters)
 export(get_class_counts)
 export(get_covariance_coverage)

NEWS

@@ -1,3 +1,6 @@
+Version 1.1.3 (DEVELOPMENT)
+ - notice:      Package namespace has been cleaned up to remove long-deprecated functions including extractModelSummaries, extractModelParameters, and extractModIndices.
+
 Version 1.1.2
  - bugfix:      Break file paths > 90 chars in prepareMplusData and mplusModeler to avoid line length errors
 

R/MplusAutomation.R

@@ -39,12 +39,6 @@
 #'   or \code{\link{LatexSummaryTable}} (returns a LaTex-formatted table of
 #'   summary statistics).
 #'
-#' Deprecated: To extract raw data created by the SAVEDATA command (e.g., class membership probabilities
-#'   or factor scores), see \code{\link{getSavedata_Data}}.
-#'
-#' Deprecated: To extract unstandardized or standardized parameter estimates from a single output file,
-#'   see \code{\link{extractModelParameters}}.
-#'
 #' Detailed model fit and parameter comparisons between two models can be obtained using
 #'   \code{\link{compareModels}}.
 #'

R/compareModels.R

@@ -5,9 +5,8 @@
 #' for filtering out fixed parameters and nonsignificant parameters. When requested, \code{compareModels}
 #' will compute the chi-square difference test for nested models (does not apply to MLMV, WLSM, and WLSMV
 #' estimators, where DIFFTEST in Mplus is needed).
-#' Model outputs to be compared can be full summaries and parameters (generated by \code{readModels}),
-#' summary statistics only (\code{extractModelSummaries}), or parameters only (\code{extractModelParameters}).
-#'
+#' 
+#' Model outputs to be compared should come from the \code{readModels} command.
 #'
 #' The \code{show} parameter can be one or more of the following, which can be passed as a vector, such as c("equal", "pdiff").
 #'
@@ -46,8 +45,7 @@
 #'   }
 #' }
 #'
-#' @param m1 The first Mplus model to be compared. Generated by \code{readModels},
-#'   	\code{extractModelSummaries}, or \code{extractModelParameters}.
+#' @param m1 The first Mplus model to be compared. Generated by \code{readModels}.
 #' @param m2 The second Mplus model to be compared.
 #' @param show What aspects of the models should be compared. Options are
 #'   	"all", "summaries", "equal", "diff", "pdiff", and "unique". See below for details.

R/extractEFAparameters.R

@@ -3,6 +3,7 @@
 #' @param outfiletext character vector of Mplus output file being processed
 #' @param filename name of the output file
 #' @return list of parsed EFA parameters
+#' @keywords internal
 extractEFAparameters <- function(outfiletext, filename) {
 
   #get pre-parsed header lines so that we demarcate the section boundaries properly

R/extractModIndices.R

@@ -123,7 +123,7 @@ extractModIndices_1file <- function(outfiletext, filename) {
   return(allSectionMI)
 }
 
-#' Extract model modification indices.
+#' (DEPRECATED) Extract model modification indices.
 #'
 #' Extracts the model modification indices from the MODEL MODIFICATION INDICES section of one
 #' or more Mplus output files. If the \code{target} is a directory, all .out files therein will be parsed
@@ -160,9 +160,8 @@ extractModIndices_1file <- function(outfiletext, filename) {
 #'   \item{StdYX_EPC}{The EPC value standardized using the variances of the continuous latent
 #'     variables as well as the variances of the background and/or outcome variables.}
 #' @author Michael Hallquist
-#' @export
 #' @seealso \code{\link{readModels}}, \code{\link{extractModelSummaries}}, \code{\link{extractModelParameters}}
-#' @keywords interface
+#' @keywords internal
 #' @examples
 #' \dontrun{
 #' ex3.14 <- extractModIndices(

R/extractParameters.R

@@ -686,7 +686,7 @@ extractParameters_1file <- function(outfiletext, filename, resultType, efa = FAL
   return(allSections)
 }
 
-#' Extract model parameters from MODEL RESULTS section.
+#' (DEPRECATED) Extract model parameters from MODEL RESULTS section.
 #'
 #' Extracts the model parameters from the MODEL RESULTS section of one or more Mplus output files.
 #' If a particular output file has more than one results section (unstandardized, stdyx, stdy, and/or std),
@@ -771,8 +771,7 @@ extractParameters_1file <- function(outfiletext, filename, resultType, efa = FAL
 #'
 #' @author Michael Hallquist
 #' @seealso \code{\link{extractModelSummaries}}
-#' @export
-#' @keywords interface
+#' @keywords internal
 #' @examples
 #' \dontrun{
 #' ex3.14 <- extractModelParameters(

R/extractSaveData.R

@@ -18,14 +18,13 @@
 #' \item{bayesVarNames}{A character vector containing the names of variables in the BPARAMETERS dataset.}
 #' \item{tech3File}{A character vector of the tech 3 output.}
 #' \item{tech4File}{A character vector of the tech 4 output.}
-#' @export
 #' @author Michael Hallquist
 #' @seealso \code{\link{getSavedata_Data}}
 #' @examples
 #' \dontrun{
 #'   fileInfo <- getSavedata_Fileinfo("C:/Program Files/Mplus/Test Output.out")
 #' }
-#' @keywords interface
+#' @keywords internal
 getSavedata_Fileinfo <- function(outfile) {
   #wraps l_getSavedata_Fileinfo by checking for the outfile and reading it as a character vector.
 
@@ -337,38 +336,18 @@ l_getSavedata_Fileinfo <- function(outfile, outfiletext, summaries) {
 #'   If \code{outfile} is a relative path or just the filename, then it is assumed that the file resides in
 #'   the working directory \code{getwd()}.
 #' @return A \code{data.frame} containing the analysis dataset generated by the SAVEDATA command.
-#' @export
 #' @author Michael Hallquist
 #' @seealso \code{\link{getSavedata_Fileinfo}}
 #' @examples
 #' \dontrun{
 #'   savedat <- getSavedata_Data("C:/Program Files/Mplus/Test Output.out")
 #' }
-#' @keywords interface
+#' @keywords internal
 getSavedata_Data <- function(outfile) {
   #exposed wrapper for l_getSavedata_Data, which pulls saveData data into data.frame
 
   message("getSavedata_Data has been deprecated. Please use readModels(\"nameofMplusoutfile.out\", what=\"savedata\")$savedata to replicate the old functionality.")
-
-#  
-#  if(!file.exists(outfile)) {
-#    stop("Cannot locate outfile: ", outfile)
-#  }
-#
-#  outfiletext <- scan(outfile, what="character", sep="\n", strip.white=FALSE, blank.lines.skip=FALSE, quiet=TRUE)
-#
-#  if (length(outfiletext) == 0) {
-#    warning("Empty outfile")
-#    return(NULL)
-#  }
-#
-#  fileInfo <- l_getSavedata_Fileinfo(outfile, outfiletext)
-#
-#  if (is.null(fileInfo) || all(is.na(fileInfo))) return(NULL)
-#  else if (is.na(fileInfo[["fileVarWidths"]][1])) return(l_getSavedata_readRawFile(outfile, outfiletext, format="free", fileName=fileInfo[["fileName"]],
-#            varNames=fileInfo[["fileVarNames"]]))
-#  else return(l_getSavedata_readRawFile(outfile, outfiletext, format="fixed", fileName=fileInfo[["fileName"]],
-#            varNames=fileInfo[["fileVarNames"]], varWidths=fileInfo[["fileVarWidths"]]))
+  return(invisible(NULL))
 }
 
 #' Load the draws from the Bayesian model posterior distribution (SAVEDATA BPARAMETERS) command into an R data.frame
@@ -392,35 +371,18 @@ getSavedata_Data <- function(outfile) {
 #' of how \code{Mplus} implements chain convergence checks and MCMC draws, see here: \url{http://www.statmodel.com/download/Bayes3.pdf}.
 #'
 #' @author Michael Hallquist, Florian Boeing-Messing
-#' @export
 #' @seealso \code{\link{getSavedata_Fileinfo}}, \code{\link{getSavedata_Data}}
 #' @references \url{http://www.statmodel.com/download/Bayes3.pdf}
 #' @examples
 #' \dontrun{
 #'   fileInfo <- getSavedata_Data("C:/Program Files/Mplus/Test Output.out")
 #' }
-#' @keywords interface
+#' @keywords internal
 getSavedata_Bparams <- function(outfile, discardBurnin=TRUE) {
   #exposed wrapper for l_getSavedata_readRawFile, which pulls bayesian parameters into a data.frame
 
   message("getSavedata_Bparams has been deprecated. Please use readModels(\"nameofMplusoutfile.out\", what=\"bparameters\")$bparameters to replicate the old functionality.")
-
-#  if(!file.exists(outfile)) {
-#    stop("Cannot locate outfile: ", outfile)
-#  }
-#
-#  outfiletext <- scan(outfile, what="character", sep="\n", strip.white=FALSE, blank.lines.skip=FALSE, quiet=TRUE)
-#
-#  if (length(outfiletext) == 0) {
-#    warning("Empty outfile")
-#    return(NULL)
-#  }
-#
-#  fileInfo <- l_getSavedata_Fileinfo(outfile, outfiletext)
-#
-#  if (is.null(fileInfo) || all(is.na(fileInfo))) return(NULL)
-#  else return(l_getSavedata_Bparams(outfile, outfiletext, fileInfo, discardBurnin=discardBurnin))
-
+  return(invisible(NULL))
 }
 
 

R/parseOutput.R

@@ -976,7 +976,7 @@ extractSummaries_1file <- function(outfiletext, filename, input)
   return(arglist)
 }
 
-#' Extract summary statistics from a single output file or from a group of Mplus models within a directory
+#' (DEPRECATED) Extract summary statistics from a single output file or from a group of Mplus models within a directory
 #'
 #' Parses a group of Mplus model output files (.out extension) for model fit statistics.
 #' At this time, the details extracted are fixed and include: \code{Filename, InputInstructions, Title, Estimator,
@@ -1048,8 +1048,7 @@ extractSummaries_1file <- function(outfiletext, filename, input)
 #'
 #' @author Michael Hallquist
 #' @seealso \code{\link{regex}}, \code{\link{runModels}}, \code{\link{readModels}}
-#' @keywords interface
-#' @export
+#' @keywords internal
 #' @examples
 #' \dontrun{
 #'   allExamples <- extractModelSummaries(