Adding the Data | Adding the Model | Adding the Posterior | Checking the final posterior, data and model | Add Posterior Reference Draws
Package: posteriordb 0.3.6
Mans Magnusson
posteriordb: R Functionality for PosteriorDB
R functionality of easy handling of the posteriordb posteriors.
Authors:
posteriordb_0.3.6.tar.gz
posteriordb_0.3.6.tgz(r-4.6-any)posteriordb_0.3.6.tgz(r-4.5-any)
posteriordb_0.3.6.tar.gz(r-4.7-any)posteriordb_0.3.6.tar.gz(r-4.6-any)
posteriordb_0.3.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
posteriordb/json (API)
| # Install 'posteriordb' in R: |
| install.packages('posteriordb', repos = c('https://staging.r-multiverse.org', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/stan-dev/posteriordb-r/issues
Last updated from:773fb7cd74. Checks:4 ERROR, 2 OK, 3 FAILURE. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | ERROR | 632 | ||
| source / vignettes | OK | 407 | ||
| linux-release-x86_64 | ERROR | 257 | ||
| macos-release-arm64 | ERROR | 167 | ||
| macos-oldrel-arm64 | ERROR | 260 | ||
| windows-devel | FAILURE | 4274 | ||
| windows-release | FAILURE | 3931 | ||
| windows-oldrel | FAILURE | 3685 | ||
| wasm-release | OK | 208 |
Exports:alias_namesas.data_infoas.model_codeas.model_infoas.pdb_dataas.pdb_data_infoas.pdb_model_codeas.pdb_model_infoas.pdb_posterioras.pdb_reference_posterior_drawsas.pdb_reference_posterior_infoas.posterioras.reference_posterior_drawsas.reference_posterior_infoas.stan_codeassert_checked_reference_posterior_drawsassert_checked_summary_statistics_drawsassert_reference_posterior_drawsbibliographycheck_pdbcheck_pdb_posteriorcheck_reference_posterior_drawscheck_summary_statistics_drawscompute_reference_posterior_drawscompute_reference_posterior_summary_statisticcompute_summary_statisticdata_file_pathdata_infodata_namesfilter_posteriorsframeworkframework<-get_datagithub_patinfoinfo<-model_codemodel_code_file_pathmodel_infomodel_namespdbpdb_bibliographypdb_configpdb_datapdb_data_infopdb_defaultpdb_githubpdb_localpdb_model_codepdb_model_infopdb_posteriorpdb_reference_posterior_drawspdb_reference_posterior_draws_infopdb_reference_posterior_infopdb_reference_posterior_summary_statisticpdb_reference_posterior_summary_statisticspdb_stan_codepdb_versionposteriorposterior_nameposterior_namesposteriors_tbl_dfreference_posterior_drawsreference_posterior_draws_file_pathreference_posterior_draws_inforeference_posterior_inforeference_posterior_namesreference_posterior_summary_statisticreference_posterior_summary_statisticsremove_pdbrename_pdbstan_codestan_code_file_pathstan_datastan_data_file_paththin_draws.pdb_reference_posterior_drawswrite_pdb
Dependencies:askpassbackportscheckmateclicurlgitcredsgluehttr2inijsonlitelifecyclemagrittropensslR6rappdirsrlangsysvctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Get all existing alias names from a posterior database | alias_names |
| Coerce a [pdb_posterior] to a Data Frame | as.data.frame.pdb_posterior as.data.frame.pdb_posteriors |
| Reference Posterior draws and summary statistics | as.pdb_reference_posterior_draws as.reference_posterior_draws as.reference_posterior_draws.draws_list as.reference_posterior_draws.stanfit assert_reference_posterior_draws pdb_reference_posterior_draws reference_posterior_draws reference_posterior_draws.character reference_posterior_draws.pdb_posterior reference_posterior_draws.pdb_reference_posterior_info |
| Assert that all checks of the reference posterior draws are true | assert_checked_reference_posterior_draws assert_checked_reference_posterior_draws.pdb_reference_posterior_draws assert_checked_reference_posterior_draws.pdb_reference_posterior_info assert_checked_summary_statistics_draws assert_checked_summary_statistics_draws.pdb_reference_posterior_draws assert_checked_summary_statistics_draws.pdb_reference_posterior_info assert_checked_summary_statistics_draws.pdb_reference_posterior_summary_statistic |
| Get the bibliography of a posterior database | bibliography pdb_bibliography |
| Check the content a posterior database | check_pdb check_pdb_aliases check_pdb_all_data_have_posterior check_pdb_all_models_have_posterior check_pdb_all_reference_posteriors_have_posterior check_pdb_posterior_references check_pdb_posterior_run_stan check_pdb_read_data check_pdb_read_model_code check_pdb_read_reference_posterior_draws check_pdb_references |
| Test a posterior | check_pdb_posterior |
| Check that reference posterior draws follows the reference posterior draws definition. | check_reference_posterior_draws check_reference_posterior_draws.character check_reference_posterior_draws.pdb_posterior check_reference_posterior_draws.pdb_reference_posterior_draws |
| Check that reference posterior draws follows the reference posterior summary definition. | check_summary_statistics_draws check_summary_statistics_draws.character check_summary_statistics_draws.pdb_posterior check_summary_statistics_draws.pdb_reference_posterior_draws |
| Compute a Reference Posteriors for a reference posterior info object | compute_reference_posterior_draws |
| Compute a Reference Posteriors using Rstan | compute_reference_posterior_draws_stan_sampling |
| Compute Summary statistics from a reference posterior | compute_reference_posterior_summary_statistic compute_summary_statistic |
| Extract data for posterior | data_file_path stan_data stan_data_file_path |
| Access data and model information | as.data_info as.data_info.list as.model_info as.model_info.list as.pdb_data_info as.pdb_model_info data_info data_info.character data_info.pdb_posterior model_info model_info.character model_info.pdb_posterior pdb_data_info pdb_model_info |
| Get all existing data names from a posterior database | data_names data_names.pdb_github data_names.pdb_local model_names.pdb_github reference_posterior_names.pdb_github |
| Filter Posteriors in Database | filter_posteriors |
| Identify the framework for a given [model_code] | framework framework.pdb_model_code framework<- framework<-.character framework<-.pdb_model_code |
| Posterior Data Sets | as.pdb_data as.pdb_data.list get_data get_data.character get_data.pdb_data_info get_data.pdb_posterior pdb_data |
| Retrieve Github personal access token. | github_pat |
| Return the name that the alias points to | handle_aliases |
| Extract information from a pdb object | info |
| Set information to a pdb object | info<- |
| Extract and construct model code objects | as.model_code as.model_code.character as.model_code.stanmodel as.pdb_model_code as.stan_code model_code model_code.character model_code.pdb_model_info model_code.pdb_posterior model_code_file_path model_code_file_path.character model_code_file_path.pdb_model_info model_code_file_path.pdb_posterior pdb_model_code pdb_stan_code stan_code stan_code_file_path |
| Get all existing model names from a posterior database | model_names model_names.pdb_local |
| Extract aliases list from posterior database | pdb_aliases |
| Assert that a file exists | pdb_assert_file_exist pdb_assert_file_exist.pdb_local |
| Returns a writable cache path for a pdb and a path It will create the directory if it does not exist. | pdb_cache_path |
| Remove object from cache | pdb_cache_rm pdb_cache_rm.pdb_data pdb_cache_rm.pdb_reference_posterior_draws |
| Read json file from 'path' | pdb_cached_local_file_path |
| Compare two stan models for the same data | pdb_compare_stan_models |
| Copy a file from a pdb to a local path | pdb_file_copy pdb_file_copy.pdb_github pdb_file_copy.pdb_local |
| Create a Posterior Database (pdb) connection | pdb pdb.character pdb.default pdb.pdb_model_code pdb_config pdb_default pdb_github pdb_local |
| Extract relevant stan versions | pdb_stan_sampling_versions |
| Get version of the 'pdb' | pdb_version pdb_version.pdb_github pdb_version.pdb_local |
| Set pdb slot | pdb<- |
| Access a posterior in the posterior database | as.pdb_posterior as.posterior as.posterior.list pdb_posterior posterior posterior.character |
| Construct dimension names from a posterior dimension list | posterior_dimension_names |
| Get all existing posterior names from a posterior database or posterior objects. | posterior_name posterior_names |
| Create Posterior Database tibbles | posteriors_tbl_df |
| Read JSON objects from the posterior database | read_json_from_pdb |
| Extract data for posterior | reference_posterior_draws_file_path reference_posterior_draws_file_path.character reference_posterior_draws_file_path.pdb_posterior reference_posterior_draws_file_path.pdb_reference_posterior_info |
| Reference posterior information | as.pdb_reference_posterior_info as.reference_posterior_info as.reference_posterior_info.list pdb_reference_posterior_draws_info pdb_reference_posterior_info reference_posterior_draws_info reference_posterior_info reference_posterior_info.character reference_posterior_info.pdb_posterior |
| Get all existing reference posterior names from a posterior database | reference_posterior_names reference_posterior_names.pdb_local |
| Reference posterior summary statistics | pdb_reference_posterior_summary_statistic pdb_reference_posterior_summary_statistics reference_posterior_summary_statistic reference_posterior_summary_statistic.character reference_posterior_summary_statistic.list reference_posterior_summary_statistic.pdb_posterior reference_posterior_summary_statistic.pdb_reference_posterior_info reference_posterior_summary_statistics reference_posterior_summary_statistics.character reference_posterior_summary_statistics.pdb_posterior |
| Remove objects from local pdb | remove_pdb remove_pdb.character remove_pdb.pdb_data remove_pdb.pdb_data_info remove_pdb.pdb_model_code remove_pdb.pdb_model_info remove_pdb.pdb_posterior remove_pdb.pdb_reference_posterior_draws remove_pdb.pdb_reference_posterior_info remove_pdb.pdb_reference_posterior_summary_statistic |
| Rename a pdb object | rename_pdb rename_pdb.pdb_data rename_pdb.pdb_posterior |
| Run Stan on a posterior | run_stan run_stan.pdb_posterior |
| Subset a [pdb_reference_posterior_draws] object | subset.pdb_reference_posterior_draws |
| Extract the type of summary statistic | summary_statistic_type |
| Thin draws to reduce their size and autocorrelation of the chains. | thin_draws.pdb_reference_posterior_draws |
| Write objects to pdb | write_pdb write_pdb.pdb_data write_pdb.pdb_data_info write_pdb.pdb_model_code write_pdb.pdb_model_info write_pdb.pdb_posterior write_pdb.pdb_reference_posterior_draws write_pdb.pdb_reference_posterior_info write_pdb.pdb_reference_posterior_summary_statistic write_pdb.stanmodel |