Package: SimNPH 0.5.9

Tobias Fellinger

SimNPH: Simulate Non-Proportional Hazards

A toolkit for simulation studies concerning time-to-event endpoints with non-proportional hazards. 'SimNPH' encompasses functions for simulating time-to-event data in various scenarios, simulating different trial designs like fixed-followup, event-driven, and group sequential designs. The package provides functions to calculate the true values of common summary statistics for the implemented scenarios and offers common analysis methods for time-to-event data. Helper functions for running simulations with the 'SimDesign' package and for aggregating and presenting the results are also included. Results of the conducted simulation study are available in the paper: "A Comparison of Statistical Methods for Time-To-Event Analyses in Randomized Controlled Trials Under Non-Proportional Hazards", Klinglmüller et al. (2025) <doi:10.1002/sim.70019>.

Authors:Tobias Fellinger [aut, cre], Florian Klinglmueller [aut]

SimNPH_0.5.9.tar.gz
SimNPH_0.5.9.zip(r-4.7-any)SimNPH_0.5.9.zip(r-4.6-any)SimNPH_0.5.9.zip(r-4.5-any)
SimNPH_0.5.9.tgz(r-4.6-any)SimNPH_0.5.9.tgz(r-4.5-any)
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SimNPH_0.5.9.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
SimNPH/json (API)

# Install 'SimNPH' in R:

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

Bug tracker:https://github.com/simnph/simnph/issues

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

Datasets:

combination_tests_delayed - Results of an example simulation

On CRAN:

clinical-trial-simulations non-proportional-hazards statistical-simulation statistics survival-analysis

5.53 score 5 stars 45 scripts 343 downloads 73 exports 117 dependencies

Last updated from:000b004438. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	205
source / vignettes	OK	227
linux-release	OK	196
macos-release	OK	241
macos-oldrel	OK	225
windows-devel	OK	104
windows-release	OK	154
windows-oldrel	OK	152
wasm-release	OK	135

Exports:admin_censoring_events admin_censoring_time analyse_aft analyse_ahr analyse_coxph analyse_describe analyse_diff_median_survival analyse_gehan_wilcoxon analyse_group_sequential analyse_logrank analyse_logrank_fh_weights analyse_maxcombo analyse_milestone_survival analyse_modelstly_weighted analyse_piecewise_exponential analyse_rmst_diff analyse_weibull assumptions_crossing_hazards assumptions_delayed_effect assumptions_progression assumptions_subgroup cen_rate_from_cen_prop_crossing_hazards cen_rate_from_cen_prop_delayed_effect cen_rate_from_cen_prop_progression cen_rate_from_cen_prop_subgroup combined_plot create_summarise_function d2m design_fixed_followup design_group_sequential generate_crossing_hazards generate_delayed_effect generate_progression generate_subgroup hazard_before_progression_from_PH_effect_size hazard_subgroup_from_PH_effect_size hr_after_crossing_from_PH_effect_size hr_after_onset_from_PH_effect_size labs_from_labels m2d m2r merge_additional_results mixture_cdf_fun mixture_cumhaz_fun mixture_haz_fun mixture_pdf_fun mixture_quant_fun mixture_rng_fun mixture_surv_fun progression_cdf_fun progression_haz_fun progression_pdf_fun progression_quant_fun progression_rate_from_progression_prop progression_surv_fun r2m random_censoring_exp recruitment_uniform rename_results_column rename_results_column_pattern results_pivot_longer shhr_gg summarise_describe summarise_estimator summarise_group_sequential summarise_test true_summary_statistics_crossing_hazards true_summary_statistics_delayed_effect true_summary_statistics_progression true_summary_statistics_subgroup upsert_merge wrap_all_in_preserve_seed wrap_all_in_trycatch

Dependencies:abind audio backports beepr boot brio broom callr car carData checkmate class cli clipr codetools colorspace cowplot cpp11 crayon Deriv desc diffobj digest doBy dplyr e1071 evaluate farver forecast Formula fracdiff fs future future.apply generics ggplot2 globals glue gtable isoband jsonlite labeling lattice lifecycle listenv lme4 lmtest magrittr MASS Matrix MatrixModels mgcv miniPCH minqa modelr muhaz multcomp mvtnorm nlme nloptr nnet nph nphRCT numDeriv otel parallelly pbapply pbkrtest pillar pkgbuild pkgconfig pkgload praise processx progressr proxy ps purrr qs2 quantreg R.methodsS3 R.oo R.utils R6 rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel Rdpack reformulas rlang rprojroot S7 sandwich scales sessioninfo SimDesign SparseM stringfish stringi stringr survival testthat TH.data tibble tidyr tidyselect timeDate urca utf8 vctrs viridisLite waldo withr zoo

Examples for the Usage of the SimNPH Package

Rendered fromsimple_example.Rmdusingknitr::rmarkdown

Last update: 2025-09-19
Started: 2022-04-28

Help page	Topics
Analyse Dataset with accelarated failure time models	analyse_aft
Analyse the dataset using extimators for the the average hazard ratio	analyse_ahr
Analyse Dataset with the Cox Protportional Hazards Model	analyse_coxph
Create a Function for Descriptive Statistics of a Dataset	analyse_describe summarise_describe
Analyse the dataset using differnce in median survival	analyse_diff_median_survival
Create Analyse function for Gehan Wilcoxon test	analyse_gehan_wilcoxon
Create Analyse Functions for Group Sequential Design	analyse_group_sequential summarise_group_sequential
Analyse Dataset with the Logrank Test	analyse_logrank
Analyse Dataset with the Fleming Harrington weighted Logrank Test	analyse_logrank_fh_weights
Analyse Dataset with the Maxcombo Test	analyse_maxcombo
Analyse the Dataset using difference or quotient of milestone survival	analyse_milestone_survival
Create Analyse function for the modestly weighted logrank test	analyse_modelstly_weighted
Create Analyse function for piecewise exponential model	analyse_piecewise_exponential
Analyse the Dataset using the difference in RMST	analyse_rmst_diff
Analyse Dataset with Weibull Regression	analyse_weibull
Create an empty assumtions data.frame for generate_progression	assumptions_progression cen_rate_from_cen_prop_progression generate_progression hazard_before_progression_from_PH_effect_size progression_rate_from_progression_prop true_summary_statistics_progression
Results of an example simulation	combination_tests_delayed
Create a summarise function from a named list of functions	create_summarise_function
Create a data.frame with an example fixed design	design_fixed_followup
Create a data.frame with an example group sequential design	design_group_sequential
Generate Dataset with crossing hazards	assumptions_crossing_hazards cen_rate_from_cen_prop_crossing_hazards generate_crossing_hazards hr_after_crossing_from_PH_effect_size true_summary_statistics_crossing_hazards
Generate Dataset with delayed effect	assumptions_delayed_effect cen_rate_from_cen_prop_delayed_effect generate_delayed_effect hr_after_onset_from_PH_effect_size true_summary_statistics_delayed_effect
Generate Dataset with different treatment effect in subgroup	assumptions_subgroup cen_rate_from_cen_prop_subgroup generate_subgroup hazard_subgroup_from_PH_effect_size true_summary_statistics_subgroup
Add ggplot axis labels from labels attribute	labs_from_labels
Fast implementation of hazard, cumulative hazard, ... for mixtures of subpopulations	mixture_cdf_fun mixture_cumhaz_fun mixture_haz_fun mixture_pdf_fun mixture_quant_fun mixture_rng_fun mixture_surv_fun
Fast implementation of cumulative density function, survival function, ... for scenarios with progression	progression_cdf_fun progression_haz_fun progression_pdf_fun progression_quant_fun progression_surv_fun
Functions to Convert Between Days and Months and Medians and Rates	d2m m2d m2r r2m
Apply Random Exponentially Distributed Censoring	random_censoring_exp
Add recruitment time to Dataset	admin_censoring_events admin_censoring_time recruitment_uniform
Rename Columns in Simulation Results and Update Attributes	rename_results_column rename_results_column_pattern
Functions for Plotting and Reporting Results	combined_plot results_pivot_longer
Plot of survival, hazard and hazard ratio of two groups as a function of time using ggplot and patchwork	shhr_gg
Generic Summarise function for esitmators	summarise_estimator
Generic summarise function for tests	summarise_test
Merge results from additional or updated simulations	merge_additional_results upsert_merge
Wrappers around Analyse Functions	wrap_all_in_preserve_seed wrap_all_in_trycatch

Package: SimNPH 0.5.9

SimNPH: Simulate Non-Proportional Hazards

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