Package: dreamer 3.2.0.9000
Richard Daniel Payne
dreamer: Dose Response Models for Bayesian Model Averaging
Fits dose-response models utilizing a Bayesian model averaging approach as outlined in Gould (2019) <doi:10.1002/bimj.201700211> for both continuous and binary responses. Longitudinal dose-response modeling is also supported in a Bayesian model averaging framework as outlined in Payne, Ray, and Thomann (2024) <doi:10.1080/10543406.2023.2292214>. Functions for plotting and calculating various posterior quantities (e.g. posterior mean, quantiles, probability of minimum efficacious dose, etc.) are also implemented. Copyright Eli Lilly and Company (2019).
Authors:
dreamer_3.2.0.9000.tar.gz
dreamer_3.2.0.9000.zip(r-4.7)dreamer_3.2.0.9000.zip(r-4.6)dreamer_3.2.0.9000.zip(r-4.5)
dreamer_3.2.0.9000.tgz(r-4.6-any)dreamer_3.2.0.9000.tgz(r-4.5-any)
dreamer_3.2.0.9000.tar.gz(r-4.7-any)dreamer_3.2.0.9000.tar.gz(r-4.6-any)
dreamer_3.2.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
dreamer/json (API)
NEWS
| # Install 'dreamer' in R: |
| install.packages('dreamer', repos = c('https://rich-payne.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/rich-payne/dreamer/issues
Pkgdown/docs site:https://rich-payne.github.io
- jags– Just Another Gibbs Sampler for Bayesian MCMC - binary JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind: * To have an engine for the BUGS language that runs on Unix * To be extensible, allowing users to write their own functions, distributions and samplers. * To be a plaftorm for experimentation with ideas in Bayesian modelling This package contains the 'jags' binary as well as the associated shared library modules loaded by the binary.
- c++– GNU Standard C++ Library v3
bayesiandose-response-modelingjagscpp
Last updated from:a16fbb0f17. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 216 | ||
| source / vignettes | OK | 234 | ||
| linux-release-x86_64 | OK | 226 | ||
| macos-release-arm64 | OK | 141 | ||
| macos-oldrel-arm64 | OK | 160 | ||
| windows-devel | OK | 210 | ||
| windows-release | OK | 196 | ||
| windows-oldrel | OK | 245 | ||
| wasm-release | OK | 112 |
Exports:diagnosticsdreamer_data_betadreamer_data_beta_binarydreamer_data_emaxdreamer_data_emax_binarydreamer_data_expdreamer_data_exp_binarydreamer_data_independentdreamer_data_independent_binarydreamer_data_lineardreamer_data_linear_binarydreamer_data_loglineardreamer_data_loglinear_binarydreamer_data_logquaddreamer_data_logquad_binarydreamer_data_quaddreamer_data_quad_binarydreamer_mcmcdreamer_plot_priormodel_betamodel_beta_binarymodel_emaxmodel_emax_binarymodel_expmodel_exp_binarymodel_independentmodel_independent_binarymodel_linearmodel_linear_binarymodel_loglinearmodel_loglinear_binarymodel_logquadmodel_logquad_binarymodel_longitudinal_idpmodel_longitudinal_itpmodel_longitudinal_linearmodel_quadmodel_quad_binaryplot_comparisonplot_tracepost_medxpost_perc_effectposteriorpr_eoipr_medpr_medx
Dependencies:clicodacpp11dplyrellipsisfarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrpillarpkgconfigpurrrR6RColorBrewerrjagsrlangrootSolveS7scalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Calculate MCMC Diagnostics for Parameters | diagnostics |
| Generate Data from Dose Response Models | dreamer_data dreamer_data_beta dreamer_data_beta_binary dreamer_data_emax dreamer_data_emax_binary dreamer_data_exp dreamer_data_exp_binary dreamer_data_independent dreamer_data_independent_binary dreamer_data_linear dreamer_data_linear_binary dreamer_data_loglinear dreamer_data_loglinear_binary dreamer_data_logquad dreamer_data_logquad_binary dreamer_data_quad dreamer_data_quad_binary |
| Bayesian Model Averaging of Dose Response Models | dreamer_mcmc |
| Plot Prior | dreamer_plot_prior |
| Posterior Plot of Bayesian Model Averaging | dreamerplot plot.dreamer_mcmc |
| Model Creation | model model_beta model_beta_binary model_emax model_emax_binary model_exp model_exp_binary model_independent model_independent_binary model_linear model_linear_binary model_loglinear model_loglinear_binary model_logquad model_logquad_binary model_quad model_quad_binary |
| Model Creation: Longitudinal Models | model_longitudinal model_longitudinal_idp model_longitudinal_itp model_longitudinal_linear |
| Compare Posterior Fits | plot_comparison plot_comparison.default plot_comparison.dreamer_bma |
| Traceplots | plot_trace |
| Posterior Distribution of Minimum X% Effective Dose | post_medx post_medx.dreamer_bma post_medx.dreamer_mcmc |
| Calculate Posterior of a Dose's Percentage Effect | post_perc_effect post_perc_effect.dreamer_bma post_perc_effect.dreamer_mcmc |
| Posterior Quantities from Bayesian Model Averaging | posterior posterior.dreamer_bma posterior.dreamer_mcmc posterior.dreamer_mcmc_independent |
| Calculate Probability of Meeting Effect of Interest (EOI) | pr_eoi |
| Pr(minimum efficacious dose) | pr_med |
| Probability of minimum X% effective dose | pr_medx |
| Summarize Bayesian Model Averaging MCMC Output | summary.dreamer_bma |
| Summarize Model Output | summary.dreamer_mcmc |
