From 7ea302fc7268bb02a2cf40d8791e895d7a0954f8 Mon Sep 17 00:00:00 2001 From: jgabry Date: Wed, 13 Mar 2024 16:40:04 -0600 Subject: [PATCH] clarify that for MCMC output_dir will contain one file per chain closes #928 --- man-roxygen/model-common-args.R | 9 +++++---- man/model-method-diagnose.Rd | 9 +++++---- man/model-method-generate-quantities.Rd | 9 +++++---- man/model-method-laplace.Rd | 9 +++++---- man/model-method-optimize.Rd | 9 +++++---- man/model-method-pathfinder.Rd | 9 +++++---- man/model-method-sample.Rd | 9 +++++---- man/model-method-sample_mpi.Rd | 9 +++++---- man/model-method-variational.Rd | 9 +++++---- 9 files changed, 45 insertions(+), 36 deletions(-) diff --git a/man-roxygen/model-common-args.R b/man-roxygen/model-common-args.R index baf67777..ca609ebe 100644 --- a/man-roxygen/model-common-args.R +++ b/man-roxygen/model-common-args.R @@ -56,10 +56,11 @@ #' method. #' #' @param output_dir (string) A path to a directory where CmdStan should write -#' its output CSV files. For interactive use this can typically be left at -#' `NULL` (temporary directory) since CmdStanR makes the CmdStan output -#' (posterior draws and diagnostics) available in \R via methods of the fitted -#' model objects. The behavior of `output_dir` is as follows: +#' its output CSV files. For MCMC there will be one file per chain; for other +#' methods there will be a single file. For interactive use this can typically +#' be left at `NULL` (temporary directory) since CmdStanR makes the CmdStan +#' output (posterior draws and diagnostics) available in \R via methods of the +#' fitted model objects. The behavior of `output_dir` is as follows: #' * If `NULL` (the default), then the CSV files are written to a temporary #' directory and only saved permanently if the user calls one of the `$save_*` #' methods of the fitted model object (e.g., diff --git a/man/model-method-diagnose.Rd b/man/model-method-diagnose.Rd index dff6359c..9a0acd31 100644 --- a/man/model-method-diagnose.Rd +++ b/man/model-method-diagnose.Rd @@ -64,10 +64,11 @@ number of chains) when called to generate the initial values. See }} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-generate-quantities.Rd b/man/model-method-generate-quantities.Rd index c9173c30..bf25602e 100644 --- a/man/model-method-generate-quantities.Rd +++ b/man/model-method-generate-quantities.Rd @@ -58,10 +58,11 @@ transformed data and the goal is to generate \emph{different} data for each chain.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-laplace.Rd b/man/model-method-laplace.Rd index 2601f558..b033fbe3 100644 --- a/man/model-method-laplace.Rd +++ b/man/model-method-laplace.Rd @@ -79,10 +79,11 @@ number of chains) when called to generate the initial values. See \item{save_latent_dynamics}{Ignored for this method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-optimize.Rd b/man/model-method-optimize.Rd index 9513db9f..dcf77444 100644 --- a/man/model-method-optimize.Rd +++ b/man/model-method-optimize.Rd @@ -93,10 +93,11 @@ temporary files created when \code{save_latent_dynamics=TRUE} see the method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-pathfinder.Rd b/man/model-method-pathfinder.Rd index db3185a3..85fc9236 100644 --- a/man/model-method-pathfinder.Rd +++ b/man/model-method-pathfinder.Rd @@ -98,10 +98,11 @@ temporary files created when \code{save_latent_dynamics=TRUE} see the method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-sample.Rd b/man/model-method-sample.Rd index ce21c60c..526c9c88 100644 --- a/man/model-method-sample.Rd +++ b/man/model-method-sample.Rd @@ -111,10 +111,11 @@ temporary files created when \code{save_latent_dynamics=TRUE} see the method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-sample_mpi.Rd b/man/model-method-sample_mpi.Rd index 8b0c3ddb..ca7203da 100644 --- a/man/model-method-sample_mpi.Rd +++ b/man/model-method-sample_mpi.Rd @@ -110,10 +110,11 @@ temporary files created when \code{save_latent_dynamics=TRUE} see the method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*} diff --git a/man/model-method-variational.Rd b/man/model-method-variational.Rd index 6b894b74..3678f11e 100644 --- a/man/model-method-variational.Rd +++ b/man/model-method-variational.Rd @@ -94,10 +94,11 @@ temporary files created when \code{save_latent_dynamics=TRUE} see the method.} \item{output_dir}{(string) A path to a directory where CmdStan should write -its output CSV files. For interactive use this can typically be left at -\code{NULL} (temporary directory) since CmdStanR makes the CmdStan output -(posterior draws and diagnostics) available in \R via methods of the fitted -model objects. The behavior of \code{output_dir} is as follows: +its output CSV files. For MCMC there will be one file per chain; for other +methods there will be a single file. For interactive use this can typically +be left at \code{NULL} (temporary directory) since CmdStanR makes the CmdStan +output (posterior draws and diagnostics) available in \R via methods of the +fitted model objects. The behavior of \code{output_dir} is as follows: \itemize{ \item If \code{NULL} (the default), then the CSV files are written to a temporary directory and only saved permanently if the user calls one of the \verb{$save_*}