Package: dreamer 3.1.0.9000
Richard Daniel Payne
dreamer: Dose Response Models for Bayesian Model Averaging
Fits (longitudinal) 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. 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_3.1.0.9000.tar.gz
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dreamer.pdf |dreamer.html✨
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
bayesiandose-response-modeling
Last updated 7 months agofrom:b1ec807399. Checks:OK: 3 NOTE: 4. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 10 2024 |
| R-4.5-win | NOTE | Oct 10 2024 |
| R-4.5-linux | NOTE | Oct 10 2024 |
| R-4.4-win | NOTE | Oct 10 2024 |
| R-4.4-mac | NOTE | Oct 10 2024 |
| R-4.3-win | OK | Oct 10 2024 |
| R-4.3-mac | OK | Oct 10 2024 |
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:clicodacolorspacecpp11dplyrellipsisfansifarvergenericsggplot2gluegtableisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigpurrrR6RColorBrewerrjagsrlangrootSolvescalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
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 |
