Package: nimbleExtra 0.1.15

Brook Milligan

nimbleExtra: Interoperating with 'NIMBLE' for Generic Analysis of MCMC Samples

'NIMBLE' is a general purpose modeling framework that facilitates the analysis of Markov Chain Monte Carlo (MCMC) models. However, it constructs a complex and variable data structure, which is difficult to use in a general way. The 'nimbleExtra' package provides a set of functions to insulate users from the complexity and variability of 'NIMBLE' data structures. It also complements 'NIMBLE' and other MCMC analysis packages by providing missing functionality to encourage generic programming. Together these features ease the burden of working with MCMC data and encourage more systematic approaches to MCMC analysis.

Authors:Brook Milligan [aut, cre, cph]

nimbleExtra_0.1.15.tar.gz
nimbleExtra_0.1.15.zip(r-4.7-any)nimbleExtra_0.1.15.zip(r-4.6-any)
nimbleExtra_0.1.15.tar.gz(r-4.7-any)nimbleExtra_0.1.15.tar.gz(r-4.6-any)
nimbleExtra_0.1.15.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
nimbleExtra/json (API)

# Install 'nimbleExtra' in R:
install.packages('nimbleExtra', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.00 score 1 scripts 247 downloads 25 exports 40 dependencies

Last updated from:9b58ab9ded. Checks:6 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develOK192
source / vignettesOK170
linux-releaseOK163
windows-develOK184
windows-releaseOK123
wasm-releaseOK117

Exports:add_predictionscoda_samplesMCMC_initial_valuesMCMC_iterationsmcmc_quantilen_chainsnimble_summarynimble_testnimble_waicposterior_keyposterior_summary_keyprint_dataframeprint_figuresprobabilitysamplesscaledselect_samplesstat_mean_ablinestat_mean_hlinestat_mean_vlinestat_quantile_linestat_quantile_ribbonstat_sample_meanstat_sample_quantilestats

Dependencies:abindbackportscheckmateclicodacpp11distributionaldplyrfarvergenericsggplot2gluegtableigraphisobandlabelinglatticelifecyclemagrittrMatrixmatrixStatsnimblenumDerivpillarpkgconfigposteriorpracmapurrrR6RColorBrewerrlangS7scalestensorAtibbletidyselectutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
nimbleExtra: Interoperating with 'NIMBLE' for Generic Analysis of MCMC SamplesnimbleExtra-package nimbleExtra
Add predictions to a dataframe of parametersadd_predictions
Extract a list of MCMC chains from NIMBLE outputcoda_samples
Sample NIMBLE datasetsexample_datasets nimble_data_m0_s0_w0_a0_c1 nimble_data_m0_s0_w0_a0_c2 nimble_data_m0_s0_w0_a1_c1 nimble_data_m0_s0_w0_a1_c2 nimble_data_m0_s0_w1_a0_c1 nimble_data_m0_s0_w1_a0_c2 nimble_data_m0_s0_w1_a1_c1 nimble_data_m0_s0_w1_a1_c2 nimble_data_m0_s1_w0_a0_c1 nimble_data_m0_s1_w0_a0_c2 nimble_data_m0_s1_w0_a1_c1 nimble_data_m0_s1_w0_a1_c2 nimble_data_m0_s1_w1_a0_c1 nimble_data_m0_s1_w1_a0_c2 nimble_data_m0_s1_w1_a1_c1 nimble_data_m0_s1_w1_a1_c2 nimble_data_m1_s0_w0_a0_c1 nimble_data_m1_s0_w0_a0_c2 nimble_data_m1_s0_w0_a1_c1 nimble_data_m1_s0_w0_a1_c2 nimble_data_m1_s0_w1_a0_c1 nimble_data_m1_s0_w1_a0_c2 nimble_data_m1_s0_w1_a1_c1 nimble_data_m1_s0_w1_a1_c2 nimble_data_m1_s1_w0_a0_c1 nimble_data_m1_s1_w0_a0_c2 nimble_data_m1_s1_w0_a1_c1 nimble_data_m1_s1_w0_a1_c2 nimble_data_m1_s1_w1_a0_c1 nimble_data_m1_s1_w1_a0_c2 nimble_data_m1_s1_w1_a1_c1 nimble_data_m1_s1_w1_a1_c2
Construct MCMC initial valuesMCMC_initial_values
Construct the total number of MCMC iterationsMCMC_iterations
Quantile(s) of a quantity across a joint distributionmcmc_quantile
Number of MCMC chainsn_chains
Extract MCMC summaries from NIMBLE outputnimble_summary
Test NIMBLEnimble_test
Extract WAIC summaries from NIMBLE outputnimble_waic
Construct a primary key for MCMC samples in posterior::draws_df formatposterior_key
Construct a primary key for MCMC samples in posterior::draws_summary formatposterior_summary_key
Print information about a dataframeprint_dataframe
Render a list of figuresprint_figures
Probability of satisfying a predicate across a joint distributionprobability
Extract a chain of MCMC samples from NIMBLE outputsamples
Add scale information to a figurescaled
Select an evenly arrayed subset of MCMC samples from a dataframeselect_samples
A ggplot2::ggplot2 stat function for the mean linear relationstat_mean_abline
A ggplot2::ggplot2 stat function for the sample meanstat_mean_hline
A ggplot2::ggplot2 stat function for the mean vline, i.e., x interceptstat_mean_vline
A 'ggplot' stat function for a single quantilestat_quantile_line
A ggplot2::ggplot2 stat function for two quantiles, min and max, defining the bounds of a ribbonstat_quantile_ribbon
A ggplot2::ggplot2 stat function for the sample meanstat_sample_mean
A ggplot2::ggplot2 stat function for a single quantilestat_sample_quantile
Extract MCMC summary statistics from MCMC samplesstats