Package: SimNPH 0.5.5

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 as preprint: "A neutral comparison of statistical methods for time-to-event analyses under non-proportional hazards", Klinglmueller et al. (2023) <doi:10.48550/ARXIV.2310.05622>.

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

SimNPH_0.5.5.tar.gz
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SimNPH.pdf |SimNPH.html✨
SimNPH/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

clinical-trial-simulationsnon-proportional-hazardsstatistical-simulationstatisticssurvival-analysis

6.40 score 6 stars 42 scripts 138 downloads 73 exports 106 dependencies

Last updated 4 months agofrom:3485630a94. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-winOKNov 14 2024
R-4.5-linuxOKNov 14 2024
R-4.4-winOKNov 14 2024
R-4.4-macOKNov 14 2024
R-4.3-winOKNov 14 2024
R-4.3-macOKNov 14 2024

Exports:admin_censoring_eventsadmin_censoring_timeanalyse_aftanalyse_ahranalyse_coxphanalyse_describeanalyse_diff_median_survivalanalyse_gehan_wilcoxonanalyse_group_sequentialanalyse_logrankanalyse_logrank_fh_weightsanalyse_maxcomboanalyse_milestone_survivalanalyse_modelstly_weightedanalyse_piecewise_exponentialanalyse_rmst_diffanalyse_weibullassumptions_crossing_hazardsassumptions_delayed_effectassumptions_progressionassumptions_subgroupcen_rate_from_cen_prop_crossing_hazardscen_rate_from_cen_prop_delayed_effectcen_rate_from_cen_prop_progressioncen_rate_from_cen_prop_subgroupcombined_plotcreate_summarise_functiond2mdesign_fixed_followupdesign_group_sequentialgenerate_crossing_hazardsgenerate_delayed_effectgenerate_progressiongenerate_subgrouphazard_before_progression_from_PH_effect_sizehazard_subgroup_from_PH_effect_sizehr_after_crossing_from_PH_effect_sizehr_after_onset_from_PH_effect_sizelabs_from_labelsm2dm2rmerge_additional_resultsmixture_cdf_funmixture_cumhaz_funmixture_haz_funmixture_pdf_funmixture_quant_funmixture_rng_funmixture_surv_funprogression_cdf_funprogression_haz_funprogression_pdf_funprogression_quant_funprogression_rate_from_progression_propprogression_surv_funr2mrandom_censoring_exprecruitment_uniformrename_results_columnrename_results_column_patternresults_pivot_longershhr_ggsummarise_describesummarise_estimatorsummarise_group_sequentialsummarise_testtrue_summary_statistics_crossing_hazardstrue_summary_statistics_delayed_effecttrue_summary_statistics_progressiontrue_summary_statistics_subgroupupsert_mergewrap_all_in_preserve_seedwrap_all_in_trycatch

Dependencies:abindaudiobackportsbeeprbootbriobroomcallrcarcarDatacheckmateclicodetoolscolorspacecowplotcpp11crayoncurlDerivdescdiffobjdigestdoBydplyrevaluatefansifarverFormulafsfuturefuture.applygenericsggplot2globalsgluegtableisobandjsonlitelabelinglatticelifecyclelistenvlme4magrittrMASSMatrixMatrixModelsmgcvmicrobenchmarkminiPCHminqamodelrmuhazmultcompmunsellmvtnormnlmenloptrnnetnphnphRCTnumDerivparallellypbapplypbkrtestpillarpkgbuildpkgconfigpkgloadpraiseprocessxprogressrpspurrrquantregR.methodsS3R.ooR.utilsR6RColorBrewerRcppRcppArmadilloRcppEigenrlangrprojrootRPushbulletsandwichscalessessioninfoSimDesignsnowSparseMstringistringrsurvivaltestthatTH.datatibbletidyrtidyselectutf8vctrsviridisLitewaldowithrzoo

Examples for the Usage of the SimNPH Package

Tobias Fellinger

Rendered fromsimple_example.Rmdusingknitr::rmarkdownon Nov 14 2024.

Last update: 2024-03-19
Started: 2022-04-28

Readme and manuals

Help Manual

Help pageTopics
Analyse Dataset with accelarated failure time modelsanalyse_aft
Analyse the dataset using extimators for the the average hazard ratioanalyse_ahr
Analyse Dataset with the Cox Protportional Hazards Modelanalyse_coxph
Create a Function for Descriptive Statistics of a Datasetanalyse_describe summarise_describe
Analyse the dataset using differnce in median survivalanalyse_diff_median_survival
Create Analyse function for Gehan Wilcoxon testanalyse_gehan_wilcoxon
Create Analyse Functions for Group Sequential Designanalyse_group_sequential summarise_group_sequential
Analyse Dataset with the Logrank Testanalyse_logrank
Analyse Dataset with the Fleming Harrington weighted Logrank Testanalyse_logrank_fh_weights
Analyse Dataset with the Maxcombo Testanalyse_maxcombo
Analyse the Dataset using difference or quotient of milestone survivalanalyse_milestone_survival
Create Analyse function for the modestly weighted logrank testanalyse_modelstly_weighted
Create Analyse function for piecewise exponential modelanalyse_piecewise_exponential
Analyse the Dataset using the difference in RMSTanalyse_rmst_diff
Analyse Dataset with Weibull Regressionanalyse_weibull
Create an empty assumtions data.frame for generate_progressionassumptions_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 simulationcombination_tests_delayed
Create a summarise function from a named list of functionscreate_summarise_function
Create a data.frame with an example fixed designdesign_fixed_followup
Create a data.frame with an example group sequential designdesign_group_sequential
Generate Dataset with crossing hazardsassumptions_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 effectassumptions_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 subgroupassumptions_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 attributelabs_from_labels
Fast implementation of hazard, cumulative hazard, ... for mixtures of subpopulationsmixture_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 progressionprogression_cdf_fun progression_haz_fun progression_pdf_fun progression_quant_fun progression_surv_fun
Functions to Convert Between Days and Months and Medians and Ratesd2m m2d m2r r2m
Apply Random Exponentially Distributed Censoringrandom_censoring_exp
Add recruitment time to Datasetadmin_censoring_events admin_censoring_time recruitment_uniform
Rename Columns in Simulation Results and Update Attributesrename_results_column rename_results_column_pattern
Functions for Plotting and Reporting Resultscombined_plot results_pivot_longer
Plot of survival, hazard and hazard ratio of two groups as a function of time using ggplot and patchworkshhr_gg
SimNPH: Simulate Non Proportional HazardsSimNPH-package SimNPH
Generic Summarise function for esitmatorssummarise_estimator
Generic summarise function for testssummarise_test
Merge results from additional or updated simulationsmerge_additional_results upsert_merge
Wrappers around Analyse Functionswrap_all_in_preserve_seed wrap_all_in_trycatch