R functionality for posteriordb

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Documentation for package ‘posteriordb’ version 0.3.2

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A B C D F G H I M P R S T W

-- A --

alias_names Get all existing alias names from a posterior database
as.data.frame.pdb_posterior Coerce a [pdb_posterior] to a Data Frame
as.data.frame.pdb_posteriors Coerce a [pdb_posterior] to a Data Frame
as.data_info Access data and model information
as.data_info.list Access data and model information
as.model_code Extract and construct model code objects
as.model_code.character Extract and construct model code objects
as.model_code.stanmodel Extract and construct model code objects
as.model_info Access data and model information
as.model_info.list Access data and model information
as.pdb_data Posterior Data Sets
as.pdb_data.list Posterior Data Sets
as.pdb_data_info Access data and model information
as.pdb_model_code Extract and construct model code objects
as.pdb_model_info Access data and model information
as.pdb_posterior Access a posterior in the posterior database
as.pdb_reference_posterior_draws Reference Posterior draws and summary statistics
as.pdb_reference_posterior_info Reference posterior information
as.posterior Access a posterior in the posterior database
as.posterior.list Access a posterior in the posterior database
as.reference_posterior_draws Reference Posterior draws and summary statistics
as.reference_posterior_draws.draws_list Reference Posterior draws and summary statistics
as.reference_posterior_draws.stanfit Reference Posterior draws and summary statistics
as.reference_posterior_info Reference posterior information
as.reference_posterior_info.list Reference posterior information
as.stan_code Extract and construct model code objects
assert_checked_reference_posterior_draws Assert that all checks of the reference posterior draws are true
assert_checked_reference_posterior_draws.pdb_reference_posterior_draws Assert that all checks of the reference posterior draws are true
assert_checked_reference_posterior_draws.pdb_reference_posterior_info Assert that all checks of the reference posterior draws are true
assert_checked_summary_statistics_draws Assert that all checks of the reference posterior draws are true
assert_checked_summary_statistics_draws.pdb_reference_posterior_draws Assert that all checks of the reference posterior draws are true
assert_checked_summary_statistics_draws.pdb_reference_posterior_info Assert that all checks of the reference posterior draws are true
assert_checked_summary_statistics_draws.pdb_reference_posterior_summary_statistic Assert that all checks of the reference posterior draws are true
assert_reference_posterior_draws Reference Posterior draws and summary statistics

-- B --

bibliography Get the bibliography of a posterior database

-- C --

check_pdb Check the content a posterior database
check_pdb_aliases Check the content a posterior database
check_pdb_all_data_have_posterior Check the content a posterior database
check_pdb_all_models_have_posterior Check the content a posterior database
check_pdb_all_reference_posteriors_have_posterior Check the content a posterior database
check_pdb_posterior Test a posterior
check_pdb_posterior_references Check the content a posterior database
check_pdb_posterior_run_stan Check the content a posterior database
check_pdb_read_data Check the content a posterior database
check_pdb_read_model_code Check the content a posterior database
check_pdb_read_reference_posterior_draws Check the content a posterior database
check_pdb_references Check the content a posterior database
check_reference_posterior_draws Check that reference posterior draws follows the reference posterior draws definition.
check_reference_posterior_draws.character Check that reference posterior draws follows the reference posterior draws definition.
check_reference_posterior_draws.pdb_posterior Check that reference posterior draws follows the reference posterior draws definition.
check_reference_posterior_draws.pdb_reference_posterior_draws Check that reference posterior draws follows the reference posterior draws definition.
check_summary_statistics_draws Check that reference posterior draws follows the reference posterior summary definition.
check_summary_statistics_draws.character Check that reference posterior draws follows the reference posterior summary definition.
check_summary_statistics_draws.pdb_posterior Check that reference posterior draws follows the reference posterior summary definition.
check_summary_statistics_draws.pdb_reference_posterior_draws Check that reference posterior draws follows the reference posterior summary definition.
compute_reference_posterior_draws Compute a Reference Posteriors for a reference posterior info object
compute_reference_posterior_draws_stan_sampling Compute a Reference Posteriors using Rstan
compute_reference_posterior_summary_statistic Compute Summary statistics from a reference posterior
compute_summary_statistic Compute Summary statistics from a reference posterior

-- D --

data_file_path Extract data for posterior
data_info Access data and model information
data_info.character Access data and model information
data_info.pdb_posterior Access data and model information
data_names Get all existing data names from a posterior database
data_names.pdb_github Get all existing data names from a posterior database
data_names.pdb_local Get all existing data names from a posterior database

-- F --

filter_posteriors Filter Posteriors in Database
framework Identify the framework for a given [model_code]
framework.pdb_model_code Identify the framework for a given [model_code]
framework<- Identify the framework for a given [model_code]
framework<-.character Identify the framework for a given [model_code]
framework<-.pdb_model_code Identify the framework for a given [model_code]

-- G --

get_data Posterior Data Sets
get_data.character Posterior Data Sets
get_data.pdb_data_info Posterior Data Sets
get_data.pdb_posterior Posterior Data Sets
github_pat Retrieve Github personal access token.

-- H --

handle_aliases Return the name that the alias points to

-- I --

info Extract information from a pdb object
info<- Set information to a pdb object

-- M --

model_code Extract and construct model code objects
model_code.character Extract and construct model code objects
model_code.pdb_model_info Extract and construct model code objects
model_code.pdb_posterior Extract and construct model code objects
model_code_file_path Extract and construct model code objects
model_code_file_path.character Extract and construct model code objects
model_code_file_path.pdb_model_info Extract and construct model code objects
model_code_file_path.pdb_posterior Extract and construct model code objects
model_info Access data and model information
model_info.character Access data and model information
model_info.pdb_posterior Access data and model information
model_names Get all existing model names from a posterior database
model_names.pdb_github Get all existing data names from a posterior database
model_names.pdb_local Get all existing model names from a posterior database

-- P --

pdb Create a Posterior Database (pdb) connection
pdb.character Create a Posterior Database (pdb) connection
pdb.default Create a Posterior Database (pdb) connection
pdb.pdb_model_code Create a Posterior Database (pdb) connection
pdb<- Set pdb slot
pdb_aliases Extract aliases list from posterior database
pdb_assert_file_exist Assert that a file exists
pdb_assert_file_exist.pdb_local Assert that a file exists
pdb_bibliography Get the bibliography of a posterior database
pdb_cached_local_file_path Read json file from 'path'
pdb_cache_path Returns a writable cache path for a pdb and a path It will create the directory if it does not exist.
pdb_cache_rm Remove object from cache
pdb_cache_rm.pdb_data Remove object from cache
pdb_cache_rm.pdb_reference_posterior_draws Remove object from cache
pdb_compare_stan_models Compare two stan models for the same data
pdb_config Create a Posterior Database (pdb) connection
pdb_data Posterior Data Sets
pdb_data_info Access data and model information
pdb_default Create a Posterior Database (pdb) connection
pdb_file_copy Copy a file from a pdb to a local path
pdb_file_copy.pdb_github Copy a file from a pdb to a local path
pdb_file_copy.pdb_local Copy a file from a pdb to a local path
pdb_github Create a Posterior Database (pdb) connection
pdb_local Create a Posterior Database (pdb) connection
pdb_model_code Extract and construct model code objects
pdb_model_info Access data and model information
pdb_posterior Access a posterior in the posterior database
pdb_reference_posterior_draws Reference Posterior draws and summary statistics
pdb_reference_posterior_draws_info Reference posterior information
pdb_reference_posterior_info Reference posterior information
pdb_reference_posterior_summary_statistic Reference posterior summary statistics
pdb_reference_posterior_summary_statistics Reference posterior summary statistics
pdb_stan_code Extract and construct model code objects
pdb_stan_sampling_versions Extract relevant stan versions
pdb_version Get version of the 'pdb'
pdb_version.pdb_github Get version of the 'pdb'
pdb_version.pdb_local Get version of the 'pdb'
posterior Access a posterior in the posterior database
posterior.character Access a posterior in the posterior database
posteriors_tbl_df Create Posterior Database tibbles
posterior_dimension_names Construct dimension names from a posterior dimension list
posterior_name Get all existing posterior names from a posterior database or posterior objects.
posterior_names Get all existing posterior names from a posterior database or posterior objects.

-- R --

read_json_from_pdb Read JSON objects from the posterior database
reference_posterior_draws Reference Posterior draws and summary statistics
reference_posterior_draws.character Reference Posterior draws and summary statistics
reference_posterior_draws.pdb_posterior Reference Posterior draws and summary statistics
reference_posterior_draws.pdb_reference_posterior_info Reference Posterior draws and summary statistics
reference_posterior_draws_file_path Extract data for posterior
reference_posterior_draws_file_path.character Extract data for posterior
reference_posterior_draws_file_path.pdb_posterior Extract data for posterior
reference_posterior_draws_file_path.pdb_reference_posterior_info Extract data for posterior
reference_posterior_draws_info Reference posterior information
reference_posterior_info Reference posterior information
reference_posterior_info.character Reference posterior information
reference_posterior_info.pdb_posterior Reference posterior information
reference_posterior_names Get all existing reference posterior names from a posterior database
reference_posterior_names.pdb_github Get all existing data names from a posterior database
reference_posterior_names.pdb_local Get all existing reference posterior names from a posterior database
reference_posterior_summary_statistic Reference posterior summary statistics
reference_posterior_summary_statistic.character Reference posterior summary statistics
reference_posterior_summary_statistic.list Reference posterior summary statistics
reference_posterior_summary_statistic.pdb_posterior Reference posterior summary statistics
reference_posterior_summary_statistic.pdb_reference_posterior_info Reference posterior summary statistics
reference_posterior_summary_statistics Reference posterior summary statistics
reference_posterior_summary_statistics.character Reference posterior summary statistics
reference_posterior_summary_statistics.pdb_posterior Reference posterior summary statistics
remove_pdb Remove objects from local pdb
remove_pdb.character Remove objects from local pdb
remove_pdb.pdb_data Remove objects from local pdb
remove_pdb.pdb_data_info Remove objects from local pdb
remove_pdb.pdb_model_code Remove objects from local pdb
remove_pdb.pdb_model_info Remove objects from local pdb
remove_pdb.pdb_posterior Remove objects from local pdb
remove_pdb.pdb_reference_posterior_draws Remove objects from local pdb
remove_pdb.pdb_reference_posterior_info Remove objects from local pdb
remove_pdb.pdb_reference_posterior_summary_statistic Remove objects from local pdb
rename_pdb Rename a pdb object
rename_pdb.pdb_data Rename a pdb object
rename_pdb.pdb_posterior Rename a pdb object
run_stan Run Stan on a posterior
run_stan.pdb_posterior Run Stan on a posterior

-- S --

stan_code Extract and construct model code objects
stan_code_file_path Extract and construct model code objects
stan_data Extract data for posterior
stan_data_file_path Extract data for posterior
subset.pdb_reference_posterior_draws Subset a [pdb_reference_posterior_draws] object
summary_statistic_type Extract the type of summary statistic

-- T --

thin_draws.pdb_reference_posterior_draws Thin draws to reduce their size and autocorrelation of the chains.

-- W --

write_pdb Write objects to pdb
write_pdb.pdb_data Write objects to pdb
write_pdb.pdb_data_info Write objects to pdb
write_pdb.pdb_model_code Write objects to pdb
write_pdb.pdb_model_info Write objects to pdb
write_pdb.pdb_posterior Write objects to pdb
write_pdb.pdb_reference_posterior_draws Write objects to pdb
write_pdb.pdb_reference_posterior_info Write objects to pdb
write_pdb.pdb_reference_posterior_summary_statistic Write objects to pdb
write_pdb.stanmodel Write objects to pdb