Package: stantargets 0.1.1.9000

William Michael Landau

stantargets: Targets for Stan Workflows

Bayesian data analysis usually incurs long runtimes and cumbersome custom code. A pipeline toolkit tailored to Bayesian statisticians, the 'stantargets' R package leverages 'targets' and 'cmdstanr' to ease these burdens. 'stantargets' makes it super easy to set up scalable Stan pipelines that automatically parallelize the computation and skip expensive steps when the results are already up to date. Minimal custom code is required, and there is no need to manually configure branching, so usage is much easier than 'targets' alone. 'stantargets' can access all of 'cmdstanr''s major algorithms (MCMC, variational Bayes, and optimization) and it supports both single-fit workflows and multi-rep simulation studies. For the statistical methodology, please refer to 'Stan' documentation (Stan Development Team 2020) <https://mc-stan.org/>.

Authors:William Michael Landau [aut, cre], Krzysztof Sakrejda [rev], Matthew T. Warkentin [rev], Eli Lilly and Company [cph]

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stantargets.pdf |stantargets.html✨
stantargets/json (API)
NEWS

# Install 'stantargets' in R:

install.packages('stantargets', repos = c('https://ropensci.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ropensci/stantargets/issues

On CRAN:

bayesian high-performance-computing make r-targetopia reproducibility stan statistics targets

29 exports 47 stars 3.08 score 54 dependencies

Last updated 9 days agofrom:448518fae3 (on main)

Exports:tar_stan_compile tar_stan_compile_run tar_stan_example_data tar_stan_example_file tar_stan_gq tar_stan_gq_rep_draws tar_stan_gq_rep_run tar_stan_gq_rep_summary tar_stan_gq_run tar_stan_mcmc tar_stan_mcmc_rep_diagnostics tar_stan_mcmc_rep_draws tar_stan_mcmc_rep_run tar_stan_mcmc_rep_summary tar_stan_mcmc_run tar_stan_mle tar_stan_mle_rep_draws tar_stan_mle_rep_run tar_stan_mle_rep_summary tar_stan_mle_run tar_stan_output tar_stan_rep_data_batch tar_stan_summary tar_stan_summary_join_data tar_stan_vb tar_stan_vb_rep_draws tar_stan_vb_rep_run tar_stan_vb_rep_summary tar_stan_vb_run

Dependencies:abind backports base64url BH callr checkmate cli cmdstanr codetools cpp11 data.table distributional dplyr evaluate fansi fs fst fstcore generics glue highr igraph jsonlite knitr lattice lifecycle magrittr Matrix matrixStats numDeriv pillar pkgconfig posterior processx ps purrr qs R6 RApiSerialize Rcpp RcppParallel rlang secretbase stringfish tarchetypes targets tensorA tibble tidyselect utf8 vctrs withr xfun yaml

Bayesian simulation pipelines with stantargets

Rendered fromsimulation.Rmdusingknitr::rmarkdownon Jul 17 2024.

Last update: 2024-04-05
Started: 2021-05-22

Introduction to stantargets

Rendered fromintroduction.Rmdusingknitr::rmarkdownon Jul 17 2024.

Last update: 2023-10-04
Started: 2021-05-22

Help page	Topics
targets: Targets Archetypes for Stan	stantargets-package
Local Stan model compilation	tar_stan_compile
Simulate example data for 'tar_stan_example_file()'.	tar_stan_example_data
Write an example Stan model file.	tar_stan_example_file
Generated quantities on an existing CmdStanFit object	tar_stan_gq
Multiple runs of generated quantities per model with draws	tar_stan_gq_rep_draws
Multiple runs of generated quantities per model with summaries	tar_stan_gq_rep_summary
One MCMC per model with multiple outputs	tar_stan_mcmc
Multiple MCMCs per model with sampler diagnostics	tar_stan_mcmc_rep_diagnostics
Multiple MCMC runs per model with draws	tar_stan_mcmc_rep_draws
Multiple MCMCs per model with summaries	tar_stan_mcmc_rep_summary
One optimization run per model with multiple outputs	tar_stan_mle
Multiple optimization runs per model with draws	tar_stan_mle_rep_draws
Multiple optimization runs per model with summaries	tar_stan_mle_rep_summary
One summary of a 'CmdStanFit' object	tar_stan_summary
One variational Bayes run per model with multiple outputs	tar_stan_vb
Multiple variational Bayes runs per model with draws	tar_stan_vb_rep_draws
Multiple iterations per model of variational Bayes with summaries	tar_stan_vb_rep_summary

Package: stantargets 0.1.1.9000

stantargets: Targets for Stan Workflows

Bayesian simulation pipelines with stantargets

Introduction to stantargets

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)