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SimNPH

Simulate Non Proportional Hazards

This package provides several functions to simulate survival data with non proportional hazards using the general purpose simulation package SimDesign.

This package follows the structure of SimDesing and provides functions that can readily be used as generate, analyse and summarise arguments in SimDesign's runSimulation function.

Usage

Installation

The current development version can be installed with:

remotes::install_git("https://github.com/SimNPH/SimNPH.git")

Getting Started

Documentation for all functions can be found in the respective help topics in the package after installation or here

Some examples of data generation, testing and estimation can be found in this vignette.

Results of the Simulation Study

The results of the simulation study done by the CONFIRMS consortium in the course of the EMA tender will be published in an upcoming paper (preprint on arXiv) and are presented in a shinylive App.

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Version

Install

install.packages('SimNPH')

Monthly Downloads

298

Version

0.5.5

License

BSL-1.0

Issues

1

Pull Requests

1

Stars

5

Forks

0

Maintainer

Tobias Fellinger

Last Published

March 4th, 2024

Functions in SimNPH (0.5.5)

analyse_milestone_survival

Analyse the Dataset using difference or quotient of milestone survival
generate_delayed_effect

Generate Dataset with delayed effect
analyse_gehan_wilcoxon

Create Analyse function for Gehan Wilcoxon test
combination_tests_delayed

Results of an example simulation
generate_crossing_hazards

Generate Dataset with crossing hazards
assumptions_progression

Create an empty assumtions data.frame for generate_progression
analyse_weibull

Analyse Dataset with Weibull Regression
design_group_sequential

Create a data.frame with an example group sequential design
generate_subgroup

Generate Dataset with different treatment effect in subgroup
design_fixed_followup

Create a data.frame with an example fixed design
create_summarise_function

Create a summarise function from a named list of functions
wrap_all_in_trycatch

Wrappers around Analyse Functions
analyse_modelstly_weighted

Create Analyse function for the modestly weighted logrank test
analyse_piecewise_exponential

Create Analyse function for piecewise exponential model
rename_results_column

Rename Columns in Simulation Results and Update Attributes
analyse_rmst_diff

Analyse the Dataset using the difference in RMST
upsert_merge

Merge results from additional or updated simulations
mixture_haz_fun

Fast implementation of hazard, cumulative hazard, ... for mixtures of subpopulations
random_censoring_exp

Apply Random Exponentially Distributed Censoring
summarise_estimator

Generic Summarise function for esitmators
summarise_test

Generic summarise function for tests
analyse_maxcombo

Analyse Dataset with the Maxcombo Test
analyse_logrank_fh_weights

Analyse Dataset with the Fleming Harrington weighted Logrank Test
labs_from_labels

Add ggplot axis labels from labels attribute
progression_cdf_fun

Fast implementation of cumulative density function, survival function, ... for scenarios with progression
r2m

Functions to Convert Between Days and Months and Medians and Rates
results_pivot_longer

Functions for Plotting and Reporting Results
shhr_gg

Plot of survival, hazard and hazard ratio of two groups as a function of time using ggplot and patchwork
analyse_aft

Analyse Dataset with accelarated failure time models
analyse_group_sequential

Create Analyse Functions for Group Sequential Design
recruitment_uniform

Add recruitment time to Dataset
analyse_diff_median_survival

Analyse the dataset using differnce in median survival
analyse_logrank

Analyse Dataset with the Logrank Test
analyse_ahr

Analyse the dataset using extimators for the the average hazard ratio
SimNPH

SimNPH: Simulate Non Proportional Hazards
analyse_describe

Create a Function for Descriptive Statistics of a Dataset
analyse_coxph

Analyse Dataset with the Cox Protportional Hazards Model