diff --git a/NAMESPACE b/NAMESPACE index 1b6530d..744afd2 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -17,6 +17,7 @@ export(HTMLSummaryTable) export(LatexSummaryTable) export(SummaryTable) export(cd) +export(checkSubmission) export(compareModels) export(createMixtures) export(createModels) @@ -94,6 +95,7 @@ importFrom(data.table,as.data.table) importFrom(data.table,fread) importFrom(data.table,fwrite) importFrom(data.table,is.data.table) +importFrom(data.table,setDF) importFrom(data.table,setnames) importFrom(digest,digest) importFrom(fastDummies,dummy_cols) diff --git a/man/checkSubmission.Rd b/man/checkSubmission.Rd index 0f434ba..c892b85 100644 --- a/man/checkSubmission.Rd +++ b/man/checkSubmission.Rd @@ -13,7 +13,7 @@ jobs to check on} \item{quiet}{If \code{TRUE}, do not print out the submission data.frame with current status} } \value{ -the \code{mplus_submission_df} with +invisibly, the \code{mplus_submission_df} with `$status` amd `$status_time` updated } \description{ check on the status of submitted Mplus jobs on the cluster diff --git a/man/l_getSavedata_readRawFile.Rd b/man/getSavedata_readRawFile.Rd similarity index 91% rename from man/l_getSavedata_readRawFile.Rd rename to man/getSavedata_readRawFile.Rd index dae8d8d..7b9872d 100644 --- a/man/l_getSavedata_readRawFile.Rd +++ b/man/getSavedata_readRawFile.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/extractSaveData.R -\name{l_getSavedata_readRawFile} -\alias{l_getSavedata_readRawFile} +\name{getSavedata_readRawFile} +\alias{getSavedata_readRawFile} \title{Internal function to load the draws from the Bayesian model posterior distribution} \usage{ -l_getSavedata_readRawFile( +getSavedata_readRawFile( outfile, outfiletext, format = "fixed", diff --git a/man/readModels.Rd b/man/readModels.Rd index 41c226a..c9ff4ee 100644 --- a/man/readModels.Rd +++ b/man/readModels.Rd @@ -66,6 +66,7 @@ a single mplus.model object, not a list of files. Specific elements are: \item{tech12}{a list containing observed versus estimated sample statistics for TYPE=MIXTURE analyses from OUTPUT: TECH12} \item{fac_score_stats}{factor score mean, correlation, and covariance structure from SAMPLE STATISTICS FOR ESTIMATED FACTOR SCORES section} \item{lcCondMeans}{conditional latent class means and pairwise comparisons, obtained using auxiliary(e) syntax in latent class models} + \item{r3step}{predictors of latent class membership using the 3-step procedure (R3STEP)} \item{gh5}{a list containing data from the gh5 (graphics) file corresponding to this output. (Requires rhdf5 package)} \item{output}{The entire, raw output file.} } diff --git a/man/submitModels.Rd b/man/submitModels.Rd index 4916762..caf8860 100644 --- a/man/submitModels.Rd +++ b/man/submitModels.Rd @@ -8,7 +8,7 @@ submitModels( target = getwd(), recursive = FALSE, filefilter = NULL, - replaceOutfile = "always", + replaceOutfile = "modifiedDate", Mplus_command = NULL, quiet = FALSE, scheduler = "slurm", @@ -23,7 +23,8 @@ submitModels( post = NULL, batch_outdir = NULL, job_script_prefix = NULL, - debug = FALSE + debug = FALSE, + fail_on_error = TRUE ) } \arguments{ @@ -88,6 +89,9 @@ a number is provided, we will treat this as the number of minutes.} \item{job_script_prefix}{the filename prefix for each job script} \item{debug}{a logical indicating whether to actually submit the jobs (TRUE) or just create the scripts for inspection (FALSE)} + +\item{fail_on_error}{Whether to stop execution of the script (TRUE), or issue a warning (FALSE) if the job +submission fails. Defaults to TRUE.} } \value{ None. Function is used for its side effects (submitting models). @@ -96,6 +100,10 @@ None. Function is used for its side effects (submitting models). This function submits a group of Mplus models (.inp files) located within a single directory or nested within subdirectories. } +\details{ +Note that if `fail_on_error` is `TRUE` and submission of one model fails, the submission loop will stop, rather than + submitting further models. +} \examples{ \dontrun{ submitModels("C:/Users/Michael/Mplus Runs", recursive=TRUE, showOutput=TRUE, @@ -105,10 +113,6 @@ single directory or nested within subdirectories. submitModels(getwd(), filefilter = "ex8.*", batch_outdir="~/mplus_batch_12") } } -\seealso{ -\code{\link{submitModels_Interactive}} -} \author{ Michael Hallquist } -\keyword{interface} diff --git a/man/summary.mplus_submission_df.Rd b/man/summary.mplus_submission_df.Rd index 0975da8..b08c130 100644 --- a/man/summary.mplus_submission_df.Rd +++ b/man/summary.mplus_submission_df.Rd @@ -4,7 +4,7 @@ \alias{summary.mplus_submission_df} \title{summary function for submission from \code{submitModels}} \usage{ -\method{summary}{mplus_submission_df}(x, refresh = FALSE) +\method{summary}{mplus_submission_df}(x, refresh = TRUE) } \arguments{ \item{x}{the \code{mplus_submission_df} object to summarize}