Package: bunsen 0.1.1

Xinlei Deng

bunsen: Marginal Survival Estimation with Covariate Adjustment

Provides an efficient and robust implementation for estimating marginal Hazard Ratio (HR) and Restricted Mean Survival Time (RMST) with covariate adjustment using Daniel et al. (2021) <doi:10.1002/bimj.201900297> and Karrison et al. (2018) <doi:10.1177/1740774518759281>.

Authors:Xinlei Deng [cre, aut], Mark Baillie [aut], Craig Wang [aut], Dominic Magirr [aut], Alex Przybylski [aut]

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

# Install 'bunsen' in R:

install.packages('bunsen', repos = c('https://openpharma.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/openpharma/bunsen/issues

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

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

oak - Oak trial data

On CRAN:

cpp

4.08 score 6 stars 3 scripts 363 downloads 13 exports 19 dependencies

Last updated from:07ba227bd2. Checks:15 OK. Indexed: yes.

Target	Result	Time
linux-devel-arm64	OK	132
linux-devel-x86_64	OK	132
source / vignettes	OK	179
linux-release-arm64	OK	103
linux-release-x86_64	OK	125
macos-release-arm64	OK	109
macos-release-x86_64	OK	313
macos-oldrel-arm64	OK	124
macos-oldrel-x86_64	OK	172
windows-devel-arm64	OK	216
windows-devel-x86_64	OK	145
windows-release-arm64	OK	194
windows-release-x86_64	OK	105
windows-oldrel-x86_64	OK	108
wasm-release	OK	88

Exports:calculate_statistics calculate_trt_effect clmqControl firstZeroIndex get_marginal_effect get_point_estimate get_rmst_estimate get_variance_estimation rbinom_matrix_vec rmst_delta rmst_point_estimate rmst_unadjust simulate_counterfactuals

Dependencies:boot cli clustermq codetools crayon globals glue hms lattice lifecycle Matrix pkgconfig prettyunits progress R6 Rcpp rlang survival vctrs

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Estimate the marginal causal survival curves using potential outcome framework	calculate_statistics
Calculate the marginal treatment effect using counterfactual simulations	calculate_trt_effect
Control of marginal HR estimation via clustermq	clmqControl
First zero index for each column of a matrix	firstZeroIndex
Calculate the marginal treatment effects for hazard ratio (HR) adjusting covariates in clinical trials	get_marginal_effect
Calculate the marginal treatment effects (only the point estimate) for hazard ratio (HR) adjusting covariates in clinical trials	get_point_estimate
Calculate the marginal restricted mean survival time (RMST) when adjusting covariates in clinical trials	get_rmst_estimate
Calculate the variance (SE) of the marginal treatment effects (hazard ratio) adjusting covariates in clinical trials	get_variance_estimation
Oak trial data	oak
Generate a matrix of binomial random values	rbinom_matrix_vec
Calculate the variance of the marginal restricted mean survival time (RMST) when adjusting covariates using the delta method	rmst_delta
Calculate the point estimate of the marginal restricted mean survival time (RMST) when adjusting covariates in clinical trials	rmst_point_estimate
Calculate the unadjusted restricted mean survival time (RMST)	rmst_unadjust
Calculate the potential outcomes using marginal survival causual curves	simulate_counterfactuals