diff --git a/DESCRIPTION b/DESCRIPTION index 44dd934..77d333e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -14,7 +14,7 @@ Description: Bayesian data analysis usually incurs long runtimes both single-fit workflows and multi-rep simulation studies. For the statistical methodology, please refer to 'Stan' documentation (Stan Development Team 2020) . -Version: 0.0.2.9000 +Version: 0.0.3 License: MIT + file LICENSE URL: https://docs.ropensci.org/stantargets/, https://github.com/ropensci/stantargets BugReports: https://github.com/ropensci/stantargets/issues diff --git a/NEWS.md b/NEWS.md index ad5c55e..66b84c6 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,6 @@ -# stantargets 0.0.2.9000 +# stantargets 0.0.3 +* Update docs to changes in `cmdstanr`, `posterior`, and `targets`. # stantargets 0.0.2 diff --git a/man/tar_stan_gq.Rd b/man/tar_stan_gq.Rd index 5cb4a71..6bf0e72 100644 --- a/man/tar_stan_gq.Rd +++ b/man/tar_stan_gq.Rd @@ -59,8 +59,11 @@ the suffixed will come from \code{names(stan_files)}.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_gq_rep.Rd b/man/tar_stan_gq_rep.Rd index 857d1f6..72c7dc0 100644 --- a/man/tar_stan_gq_rep.Rd +++ b/man/tar_stan_gq_rep.Rd @@ -59,8 +59,11 @@ files created before running the pipeline.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_gq_rep_draws.Rd b/man/tar_stan_gq_rep_draws.Rd index c457557..f8a444e 100644 --- a/man/tar_stan_gq_rep_draws.Rd +++ b/man/tar_stan_gq_rep_draws.Rd @@ -55,8 +55,11 @@ files created before running the pipeline.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_gq_rep_run.Rd b/man/tar_stan_gq_rep_run.Rd index 2a77762..f1ac484 100644 --- a/man/tar_stan_gq_rep_run.Rd +++ b/man/tar_stan_gq_rep_run.Rd @@ -44,8 +44,11 @@ it is more convenient to specify the Stan program as a string.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_gq_rep_summary.Rd b/man/tar_stan_gq_rep_summary.Rd index 30de852..21e3625 100644 --- a/man/tar_stan_gq_rep_summary.Rd +++ b/man/tar_stan_gq_rep_summary.Rd @@ -57,8 +57,11 @@ files created before running the pipeline.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_gq_run.Rd b/man/tar_stan_gq_run.Rd index 012bf18..65725ca 100644 --- a/man/tar_stan_gq_run.Rd +++ b/man/tar_stan_gq_run.Rd @@ -34,8 +34,11 @@ it is more convenient to specify the Stan program as a string.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_mcmc_rep_run.Rd b/man/tar_stan_mcmc_rep_run.Rd index 195e9fe..33c9e6f 100644 --- a/man/tar_stan_mcmc_rep_run.Rd +++ b/man/tar_stan_mcmc_rep_run.Rd @@ -66,8 +66,11 @@ it is more convenient to specify the Stan program as a string.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_mcmc_run.Rd b/man/tar_stan_mcmc_run.Rd index d790334..d638263 100644 --- a/man/tar_stan_mcmc_run.Rd +++ b/man/tar_stan_mcmc_run.Rd @@ -56,8 +56,11 @@ it is more convenient to specify the Stan program as a string.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_mle.Rd b/man/tar_stan_mle.Rd index 95b6c17..3c0c213 100644 --- a/man/tar_stan_mle.Rd +++ b/man/tar_stan_mle.Rd @@ -68,8 +68,11 @@ the suffixed will come from \code{names(stan_files)}.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_mle_rep.Rd b/man/tar_stan_mle_rep.Rd index 83bda6a..00ad9b7 100644 --- a/man/tar_stan_mle_rep.Rd +++ b/man/tar_stan_mle_rep.Rd @@ -67,8 +67,11 @@ files created before running the pipeline.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_mle_rep_draws.Rd b/man/tar_stan_mle_rep_draws.Rd index 1c8ebf3..920dec3 100644 --- a/man/tar_stan_mle_rep_draws.Rd +++ b/man/tar_stan_mle_rep_draws.Rd @@ -64,8 +64,11 @@ files created before running the pipeline.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_mle_rep_run.Rd b/man/tar_stan_mle_rep_run.Rd index bba5ad1..514af54 100644 --- a/man/tar_stan_mle_rep_run.Rd +++ b/man/tar_stan_mle_rep_run.Rd @@ -49,8 +49,11 @@ it is more convenient to specify the Stan program as a string.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_mle_rep_summary.Rd b/man/tar_stan_mle_rep_summary.Rd index 792c631..1fa6699 100644 --- a/man/tar_stan_mle_rep_summary.Rd +++ b/man/tar_stan_mle_rep_summary.Rd @@ -66,8 +66,11 @@ files created before running the pipeline.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_mle_run.Rd b/man/tar_stan_mle_run.Rd index 70f4650..a8b7256 100644 --- a/man/tar_stan_mle_run.Rd +++ b/man/tar_stan_mle_run.Rd @@ -43,8 +43,11 @@ it is more convenient to specify the Stan program as a string.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_vb.Rd b/man/tar_stan_vb.Rd index 51fb6de..e13d615 100644 --- a/man/tar_stan_vb.Rd +++ b/man/tar_stan_vb.Rd @@ -69,8 +69,11 @@ the suffixed will come from \code{names(stan_files)}.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_vb_rep.Rd b/man/tar_stan_vb_rep.Rd index 14ac0d2..0feb2b8 100644 --- a/man/tar_stan_vb_rep.Rd +++ b/man/tar_stan_vb_rep.Rd @@ -68,8 +68,11 @@ files created before running the pipeline.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_vb_rep_draws.Rd b/man/tar_stan_vb_rep_draws.Rd index fa2dc41..a1e9d38 100644 --- a/man/tar_stan_vb_rep_draws.Rd +++ b/man/tar_stan_vb_rep_draws.Rd @@ -65,8 +65,11 @@ files created before running the pipeline.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_vb_rep_run.Rd b/man/tar_stan_vb_rep_run.Rd index 29c40b8..8bbacee 100644 --- a/man/tar_stan_vb_rep_run.Rd +++ b/man/tar_stan_vb_rep_run.Rd @@ -54,8 +54,11 @@ it is more convenient to specify the Stan program as a string.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_vb_rep_summary.Rd b/man/tar_stan_vb_rep_summary.Rd index b143c2e..9a0164d 100644 --- a/man/tar_stan_vb_rep_summary.Rd +++ b/man/tar_stan_vb_rep_summary.Rd @@ -67,8 +67,11 @@ files created before running the pipeline.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block. diff --git a/man/tar_stan_vb_run.Rd b/man/tar_stan_vb_run.Rd index 4b97b35..e6c2387 100644 --- a/man/tar_stan_vb_run.Rd +++ b/man/tar_stan_vb_run.Rd @@ -44,8 +44,11 @@ it is more convenient to specify the Stan program as a string.} \item{data}{(multiple options) The data to use for the variables specified in the data block of the Stan program. One of the following: \itemize{ -\item A named list of \R objects (like for RStan). Internally this list is then -written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. +\item A named list of \R objects with the names corresponding to variables +declared in the data block of the Stan program. Internally this list is then +written to JSON for CmdStan using \code{\link[cmdstanr:write_stan_json]{write_stan_json()}}. See +\code{\link[cmdstanr:write_stan_json]{write_stan_json()}} for details on the conversions performed on \R objects +before they are passed to Stan. \item A path to a data file compatible with CmdStan (JSON or \R dump). See the appendices in the CmdStan manual for details on using these formats. \item \code{NULL} or an empty list if the Stan program has no data block.