Package: drugdevelopR 1.0.2

Lukas D. Sauer

drugdevelopR: Utility-Based Optimal Phase II/III Drug Development Planning

Plan optimal sample size allocation and go/no-go decision rules for phase II/III drug development programs with time-to-event, binary or normally distributed endpoints when assuming fixed treatment effects or a prior distribution for the treatment effect, using methods from Kirchner et al. (2016) <doi:10.1002/sim.6624> and Preussler (2020). Optimal is in the sense of maximal expected utility, where the utility is a function taking into account the expected cost and benefit of the program. It is possible to extend to more complex settings with bias correction (Preussler S et al. (2020) <doi:10.1186/s12874-020-01093-w>), multiple phase III trials (Preussler et al. (2019) <doi:10.1002/bimj.201700241>), multi-arm trials (Preussler et al. (2019) <doi:10.1080/19466315.2019.1702092>), and multiple endpoints (Kieser et al. (2018) <doi:10.1002/pst.1861>).

Authors:Stella Erdmann [aut], Johannes Cepicka [aut], Marietta Kirchner [aut], Meinhard Kieser [aut], Lukas D. Sauer [aut, cre]

drugdevelopR_1.0.2.tar.gz
drugdevelopR_1.0.2.zip(r-4.7)drugdevelopR_1.0.2.zip(r-4.6)drugdevelopR_1.0.2.zip(r-4.5)
drugdevelopR_1.0.2.tgz(r-4.6-any)drugdevelopR_1.0.2.tgz(r-4.5-any)
drugdevelopR_1.0.2.tar.gz(r-4.7-any)drugdevelopR_1.0.2.tar.gz(r-4.6-any)
drugdevelopR_1.0.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
drugdevelopR/json (API)

# Install 'drugdevelopR' in R:
install.packages('drugdevelopR', repos = c('https://sterniii3.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sterniii3/drugdevelopr/issues

Pkgdown/docs site:https://sterniii3.github.io

On CRAN:

Conda:

5.69 score 3 stars 15 scripts 290 downloads 120 exports 26 dependencies

Last updated from:dbead106b3. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
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source / vignettesOK245
linux-release-x86_64OK287
macos-release-arm64OK324
macos-oldrel-arm64OK300
windows-develOK294
windows-releaseOK277
windows-oldrelOK263
wasm-releaseOK160

Exports:d3_skipII_ttedbivanormdrugdevelopRdrugdevelopResultEd3_LEd3_L2Ed3_REd3_R2Ed3_tteEn3_binary_LEn3_binary_L2En3_binary_REn3_binary_R2En3_normal_LEn3_normal_L2En3_normal_REn3_normal_R2Epgo_binary_L2Epgo_binary_R2Epgo_L2Epgo_normal_L2Epgo_normal_R2Epgo_R2Epgo_tteEpgo23Epgo23_binaryEpgo23_normalEPsProg_binary_LEPsProg_binary_L2EPsProg_binary_REPsProg_binary_R2EPsProg_LEPsProg_L2EPsProg_multiple_normalEPsProg_multiple_tteEPsProg_normal_LEPsProg_normal_L2EPsProg_normal_REPsProg_normal_R2EPsProg_REPsProg_R2EPsProg_tteEPsProg2EPsProg2_binaryEPsProg2_normalEPsProg23EPsProg23_binaryEPsProg23_normalEPsProg3EPsProg3_binaryEPsProg3_normalEPsProg4EPsProg4_binaryEPsProg4_normalEss_binaryEss_multiple_normalEss_multiple_tteEss_normalEss_ttefmaxfminoptimal_biasoptimal_bias_binaryoptimal_bias_normaloptimal_binaryoptimal_multiarmoptimal_multiarm_binaryoptimal_multiarm_normaloptimal_multiple_normaloptimal_multiple_tteoptimal_multitrialoptimal_multitrial_binaryoptimal_multitrial_normaloptimal_normaloptimal_tteos_ttepgo_binarypgo_multiple_normalpgo_multiple_ttepgo_normalpgo_tteposp_normalprior_ttePsProg_binaryPsProg_normalPsProg_ttepwss_binaryss_normalss_tteutility_binary_Lutility_binary_L2utility_binary_Rutility_binary_R2utility_Lutility_L2utility_multiarmutility_multiarm_binaryutility_multiarm_normalutility_multiple_normalutility_multiple_tteutility_normal_Lutility_normal_L2utility_normal_Rutility_normal_R2utility_Rutility_R2utility_tteutility2utility2_binaryutility2_normalutility23utility23_binaryutility23_normalutility3utility3_binaryutility3_normalutility4utility4_binaryutility4_normal

Dependencies:clicodetoolscubaturedigestdoParallelexpmforeachgenericsglueiteratorslatticelifecyclemagrittrMASSMatrixmsmmvtnormpillarpkgconfigprogressrRcpprlangsurvivaltibbleutf8vctrs

Package validation
Guide to running the validation suite | Adding a signature page | References
Rendered fromPackage_validation.Rmdusingknitr::rmarkdown

Last update: 2025-01-14
Started: 2023-04-17

Bias adjustment - methods for discounting of phase II results
The example setting | Applying the package to the example | Interpreting the output | Where to go from here | References
Rendered fromBias_adjustment.Rmdusingknitr::rmarkdown

Last update: 2023-12-20
Started: 2022-12-31

Binary outcome variables
The example setting | Applying the package to the example | Defining all necessary parameters | Interpreting the output | Where to go from here
Rendered fromBinary_outcomes.Rmdusingknitr::rmarkdown

Last update: 2023-12-20
Started: 2023-03-30

Fixed effect estimates and prior distributions
The example setting | Parameters of the prior distribution | Interpreting the output | Prior distributions for time-to-event outcomes | Where to go from here
Rendered fromFixed_and_prior_distributions.Rmdusingknitr::rmarkdown

Last update: 2023-12-20
Started: 2022-12-04

Interpreting the rest of the output
The example setting and the input parameters | Interpreting the output | Where to go from here
Rendered fromInterpreting_Output.Rmdusingknitr::rmarkdown

Last update: 2023-12-20
Started: 2022-12-13

Multiarm - methods for multi-arm programs
The example setting | Applying the package to the example | Defining all necessary parameters | Interpreting the output | Where to go from here
Rendered fromMultiarm_Trials.Rmdusingknitr::rmarkdown

Last update: 2023-12-20
Started: 2022-12-31

Multiple - methods for trials with multiple endpoints
Only one endpoint has to be significant | Defining all necessary parameters | Interpreting the output | Both endpoints have to be significant | Where to go from here
Rendered fromMultiple_Endpoints.Rmdusingknitr::rmarkdown

Last update: 2023-12-20
Started: 2022-12-31

More parameters to adapt to specific settings
The example setting and the input parameters | Fixed treatment effect estimates or prior distributions | Constrained optimization | Cost constraint -- maximum total costs | Sample size constraint -- maximum number of participants | Success probability constraint - minimum probability of a successful program | Customized effect size categories | Differences in the treatment effect | Skipping phase II | Parallel computing | Where to go from here | References
Rendered fromMore_Parameters.Rmdusingknitr::rmarkdown

Last update: 2023-12-20
Started: 2022-12-28

Multitrial - methods for programs with several phase III trials
The example setting | Applying the package to the example | Interpreting the output | Where to go from here | References
Rendered fromMultitrial.Rmdusingknitr::rmarkdown

Last update: 2023-12-20
Started: 2022-12-31

Time-to-event outcome variables
The example setting | Applying the package to the example | Defining all necessary parameters | Interpreting the output | Where to go from here
Rendered fromTime-to-event_outcomes.Rmdusingknitr::rmarkdown

Last update: 2023-12-20
Started: 2022-12-31

Introduction to planning phase II and phase III trials with drugdevelopR
The example setting | Applying the package to the example | Defining all necessary parameters | Interpreting the output | Where to go from here
Rendered fromIntroduction-to-drugdevelopR.Rmdusingknitr::rmarkdown

Last update: 2023-09-22
Started: 2023-04-18

Readme and manuals

Help Manual

Help pageTopics
Optimal phase II/III drug development planning for time-to-event endpoints when discounting phase II resultsoptimal_bias
Optimal phase II/III drug development planning when discounting phase II results with binary endpointoptimal_bias_binary
Optimal phase II/III drug development planning when discounting phase II results with normally distributed endpointoptimal_bias_normal
Optimal phase II/III drug development planning with binary endpointoptimal_binary
Optimal phase II/III drug development planning for multi-arm programs with time-to-event endpointoptimal_multiarm
Optimal phase II/III drug development planning for multi-arm programs with binary endpointoptimal_multiarm_binary
Optimal phase II/III drug development planning for multi-arm programs with normally distributed endpointoptimal_multiarm_normal
Optimal phase II/III drug development planning for programs with multiple normally distributed endpointsoptimal_multiple_normal
Optimal phase II/III drug development planning for programs with multiple time-to-event endpointsoptimal_multiple_tte
Optimal phase II/III drug development planning where several phase III trials are performed for time-to-event endpointsoptimal_multitrial
Optimal phase II/III drug development planning where several phase III trials are performedoptimal_multitrial_binary
Optimal phase II/III drug development planning where several phase III trials are performedoptimal_multitrial_normal
Optimal phase II/III drug development planning with normally distributed endpointoptimal_normal
Optimal phase II/III drug development planning with time-to-event endpointoptimal_tte