updating the function list in package, dropping unused rd files

R/deprecated.r

@@ -261,6 +261,10 @@ twoGroupOrdinal <- function(modelName ="Ordinal", selDVs, factorLevels, dzData,
 	stop("Change \"twoGroupOrdinal\" to: makeOrdinal_2Group")
 }
 
+umxGraph_RAM <- function(model = NA, std = T, precision = 2, dotFilename = "name", pathLabels = "none", showFixed = F, showError = T) {
+	stop("Replace umxGraph_RAM with umxPlot (umxGraph_RAM was deprecated to help people learn umx more quickly)")
+}
+
 tryHard <- function(model, n = 3, calc_SE = F){stop("Use umxRun() in place of umxTryHard() and tryHard()")}
 
 genEpi_ReRun <- function(lastFit, dropList=NA, regex=NA, free=F, value=0, freeToStart=NA, newName=NA, verbose=F, intervals=F) {message("please call umxReRun()")}
@@ -305,4 +309,9 @@ stringToMxAlgebra <- function(algString, name = NA, dimnames = NA) {
 
 genEpi_EvalQuote <- function(expstring, model, compute, show){
 	stop("Deprecated: Please replace genEpi_EvalQuote with umxEval")
-}
+}
+
+
+umxReportCIs <- function(model = NA, addCIs = T, runCIs = "if necessary") {
+	stop("Deprecated: Please replace umxReportCIs with umxCI")
+}

R/fit_and_reporting.r

@@ -54,6 +54,26 @@ umxCompare <- function(base = NULL, comparison = NULL, all = TRUE, output = "ret
 	# }
 }
 
+#' extractAIC
+#'
+#' returns the AIC for an OpenMx model
+#'
+#' @param model an \code{\link{mxModel}} to get the AIC for
+#' @return - AIC value
+#' @export
+#' @seealso - \code{\link{umxRun}}, \code{\link{umxCompare}}
+#' @references - \url{http://openmx.psyc.virginia.edu}
+#' @examples
+#' \dontrun{
+#' x = extractAIC(model)
+#' }
+extractAIC.MxModel <- function(model) {
+	require(umx)
+	a = umx::umxCompare(model)
+	return(a[1,"AIC"])
+}
+
+
 #' umxSummary
 #'
 #' Report the fit of a model in a compact form suitable for a journal. Emits a "warning" not 
@@ -171,9 +191,9 @@ umxSummary <- function(model, saturatedModels = NULL, report = "line", showEstim
 	})
 }
 
-#' umxReportCIs
+#' umxCI
 #'
-#' umxReportCIs umxReportCIs adds mxCI() calls for all free parameters in a model, 
+#' umxCI adds mxCI() calls for all free parameters in a model, 
 #' runs the CIs, and reports a neat summary.
 #'
 #' This function also reports any problems computing a CI. The codes are standard OpenMx errors and warnings
@@ -200,10 +220,10 @@ umxSummary <- function(model, saturatedModels = NULL, report = "line", showEstim
 #' umxReportCIs(model)
 #' }
 
-umxReportCIs <- function(model = NA, addCIs = T, runCIs = "if necessary") {
+umxCI <- function(model = NA, addCIs = T, runCIs = "if necessary") {
 	# TODO add code to not-run CIs
 	if(is.na(model)){
-		message("umxReportCIs adds mxCI() calls for all free parameters in a model, runs them, and reports a neat summary. A use example is:\n umxReportCIs(model)")
+		message("umxCI adds mxCI() calls for all free parameters in a model, runs them, and reports a neat summary. A use example is:\n umxReportCIs(model)")
 		stop();
 	}
 	message("### CIs for model ", model@name)

R/xmu.r

@@ -467,7 +467,3 @@ xmuMI <- function(model, vector = T) {
 	close(bar)
 	return(ret)
 }
-
-umxGraph_RAM <- function(model = NA, std = T, precision = 2, dotFilename = "name", pathLabels = "none", showFixed = F, showError = T) {
-	stop("Replace umxGraph_RAM with umxPlot (umxGraph_RAM was deprecated to help people learn umx more quickly)")
-}

man/umx-package.Rd

@@ -30,22 +30,31 @@ library("umx")
 
 \bold{Index:}
 
-\bold{Build, Run, and Report}
+\bold{Build and Run a Model}
 
 \code{\link{umxLabel}}                Add labels to all parameters of a model
 
 \code{\link{umxStart}}                Set sensible start values
 
 \code{\link{umxRun}}                  Run a model, adding saturated models if necessary, optionally adds labels and starts
 
-\code{\link{umxCompare}}              Compare one or more models
+\code{\link{umxLatent}}               Create a latent variable, taking care of reflective/formative distinctions automagically
 
-\code{\link{umxSummary}}              Compact report of model fit
+\code{\link{umxSaturated}}            Create saturated and independence models so that reporting works. (called from umxRun for you)
 
-\code{\link{umxCI}}                  Report FIML CIs on a model, creating them if necessary
+\bold{Get reports of model results}
+
+\code{\link{umxSummary}}             Compact report of model fit
 
 \code{\link{umxPlot}}                Create a Path Diagram from your model!
 
+\code{\link{umxCompare}}             Compare one or more models
+
+\code{\link{umxCI}}                  Add and report FIML Confidence Intervals for a model.
+
+\code{\link{extractAIC.MxModel}}     Report the AIC for a model.
+
+
 
 \bold{Updating & Modifying}
 
@@ -59,12 +68,18 @@ library("umx")
 
 \code{\link{umxMI}}                   Compute modification indices for RAM models
 
+\code{\link{umxGetParameters}}        A regex enabled version of \code{\link{mxGetParameters}}
+
 \bold{High-level reporting}
 
-\code{\link{umxUnexplainedCausalNexus}}
+\code{\link{umxUnexplainedCausalNexus}} Compute the change in an outcome variable that flows from a change in an input
+
+
 
 \bold{Utilities}
 
+\code{\link{umxUpdateOpenMx}}         umxUpdateOpenMx
+
 \code{\link{umxStandardizeModel}}     Standardize a RAM Model
 
 \code{\link{umxReportTime}}           Show how long a model took to run
@@ -73,23 +88,49 @@ library("umx")
 
 \code{\link{umxJiggle}}               Jiggle values in a list
 
-\code{\link{umxUpdateOpenMx}}         umxUpdateOpenMx
-
 \code{\link{umxHasCIs}}               Utility function to ask a model if it has CIs
 
-\code{\link{umxIsMxModel}}            Utility function to an object "Are you an OpenMx model?"
+\code{\link{umxIsMxModel}}            Utility function to ask an object "Are you an OpenMx model?"
+
+\code{\link{umxIsRAMmodel}}           Utility function to ask an object "Are you an OpenMx RAM model?"
+
+\code{\link{umxIsOrdinalVar}}         Utility function to ask an object "Are you an ordinal variable?"
 
-\code{\link{umxIsRAMmodel}}            Utility function to an object "Are you an OpenMx RAM model?"
+\code{\link{umx_find_object}}         Find an OpenMx (or other) object by name
+
+\code{\link{umx_grep_labels}}         Find labels (SPSS-style) which match a regular expression. Useful.
+
+\code{\link{umxCov2cor}}              Convert a covariance matrix to a corelation matrix, guaranteeing the upper and lower triangles are exact equal
+
+\code{\link{umx_is_cov}}              Test if data is a covariance matrix
+
+\code{\link{umx_reorder}}             Reorder the variables in a covariance matrix (including dropping variables)
+
+\code{\link{umxLower2full}}          Take a lower matrix and populate the upper triangle
 
 \bold{Non-SEM helpers}
 
-\code{\link{print.dataframe}}         print dataframe in readable form by supressing NA and rounding 0
+\code{\link{umx_swap_a_block}}        Swap places with one block of data to another
+
+\code{\link{umx_move_file.Rd}}       Flexibly move files on the filesystem
+
+\code{\link{umx_rename_file.Rd}}      Flexibly rename files on the filsystem
+
+\code{\link{umx_greater_than}}        A version of %>% which excludes NA
+
+\code{\link{umx_less_than}}           A version of %<% which excludes NA
+
+\code{\link{umx_cor}}                 Report correlations and their p-values
+
+\code{\link{print.dataframe}}         Print dataframe in readable form by supressing NAs, rounding numbers, and presenting zeros as "0"
 
 \code{\link{umxAnovaReport}}          Format an anova model into an APA-style report
 
 \code{\link{Stouffer.test}}           Run a Stouffer.test (meta-analytic p-value)
 
-\code{\link{umx_u_APA_pval}}          Utility function to format a p-value for APA (three decimals, "<.001" if under that)
+\code{\link{umx_APA_pval}}            Utility function to format a p-value for APA (three decimals, "<.001" if under that)
+
+\code{\link{umx_round}}               Control rounding in ways of more use to scientists than computers
 
 \code{\link{umxDescriptives}}         Utility function to generate participant section for an APA-style article.