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:Richard Daniel Payne [aut, cre], William Michael Landau [rev], Mitch Thomann [rev], Eli Lilly and Company [cph]

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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
dreamer/json (API)

# 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

Uses libs:
  • jags– Just Another Gibbs Sampler for Bayesian MCMC
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

bayesiandose-response-modelingjagscpp

5.00 score 10 stars 8 scripts 364 downloads 46 exports 34 dependencies

Last updated from:a16fbb0f17. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK238
source / vignettesOK280
linux-release-x86_64OK228
macos-release-arm64OK174
macos-oldrel-arm64OK135
windows-develOK241
windows-releaseOK216
windows-oldrelOK206
wasm-releaseOK125

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

Dose REsponse models for bAyesian Model avERaging (dreamer)
dreamer | Generate data | Fit Model | Model Output | Posterior Credible Intervals | Posterior Plots | Posterior Quantities | Probability of Meeting Effect of Interest (EOI) | Probability of Minimum Efficacious Dose (MED) | Probability of Minimum Dose with at Least X% Efficacy | Posterior Probability of MEDX | Posterior Distribution of Percentage Effect | MCMC Diagnostics | Visualizing Priors | Independent Model | Longitudinal Modeling | Reference
Rendered fromdreamer.Rmdusingknitr::rmarkdown

Last update: 2022-08-30
Started: 2021-08-16

dreamer Methods
Bayesian Model Averaging in dreamer | Reference
Rendered fromdreamer_method.Rmdusingknitr::rmarkdown

Last update: 2022-07-12
Started: 2021-08-20

Readme and manuals

Help Manual

Help pageTopics
Calculate MCMC Diagnostics for Parametersdiagnostics
Generate Data from Dose Response Modelsdreamer_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 Modelsdreamer_mcmc
Plot Priordreamer_plot_prior
Posterior Plot of Bayesian Model Averagingdreamerplot plot.dreamer_mcmc
Model Creationmodel 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 Modelsmodel_longitudinal model_longitudinal_idp model_longitudinal_itp model_longitudinal_linear
Compare Posterior Fitsplot_comparison plot_comparison.default plot_comparison.dreamer_bma
Traceplotsplot_trace
Posterior Distribution of Minimum X% Effective Dosepost_medx post_medx.dreamer_bma post_medx.dreamer_mcmc
Calculate Posterior of a Dose's Percentage Effectpost_perc_effect post_perc_effect.dreamer_bma post_perc_effect.dreamer_mcmc
Posterior Quantities from Bayesian Model Averagingposterior 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 dosepr_medx
Summarize Bayesian Model Averaging MCMC Outputsummary.dreamer_bma
Summarize Model Outputsummary.dreamer_mcmc