Package: simaerep 0.6.1

Bjoern Koneswarakantha

simaerep: Find Clinical Trial Sites Under-Reporting Adverse Events

Monitoring of Adverse Event (AE) reporting in clinical trials is important for patient safety. Sites that are under-reporting AEs can be detected using Bootstrap-based simulations that simulate overall AE reporting. Based on the simulation an AE under-reporting probability is assigned to each site in a given trial (Koneswarakantha 2021 <doi:10.1007/s40264-020-01011-5>).

Authors:Bjoern Koneswarakantha [aut, cre, cph], F. Hoffmann-La Roche Ltd [cph]

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NEWS

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

Peer review:

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

On CRAN:

ae-reportingclinical-trials

5.20 score 21 stars 25 scripts 475 downloads 38 exports 54 dependencies

Last updated 2 months agofrom:fa10836cd0. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 01 2024
R-4.5-winOKNov 01 2024
R-4.5-linuxOKNov 01 2024
R-4.4-winOKNov 02 2024
R-4.4-macOKNov 01 2024
R-4.3-winOKNov 01 2024
R-4.3-macOKNov 02 2024

Exports:%>%aggr_duplicated_visitscheck_df_visiteval_sitesexp_implicit_missing_visitsget_configget_ecd_valuesget_pat_pool_configget_portf_perfis_orivisitis_simaerepmax_rankorivisitpat_aggrpat_poolplot_dotsplot_sim_exampleplot_sim_examplesplot_studyplot_visit_med75poiss_test_site_ae_vs_study_aeprep_for_simprob_lower_site_ae_vs_study_aepurrr_barsim_after_prepsim_inframesim_scenariosim_sitessim_studiessim_test_data_patientsim_test_data_portfoliosim_test_data_studysim_ursim_ur_scenariossimaerepsimaerep_inframesite_aggrwith_progress_cnd

Dependencies:blobclicodetoolscolorspacecowplotcpp11DBIdbplyrdigestdplyrevaluatefansifarverforcatsfurrrfuturegenericsggplot2globalsgluegtablehighrisobandknitrlabelinglatticelifecyclelistenvmagrittrMASSMatrixmgcvmunsellnlmeparallellypillarpkgconfigprogressrpurrrR6RColorBrewerrlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithrxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Aggregate duplicated visits.aggr_duplicated_visits
Integrity check for df_visit.check_df_visit
Evaluate sites.eval_sites
Expose implicitly missing visits.exp_implicit_missing_visits
Get Portfolio Configurationget_config
Get empirical cumulative distribution values of pval or prob_lowerget_ecd_values
Configure study patient pool by site parameters.get_pat_pool_config
Get Portfolio Performanceget_portf_perf
Get site mean ae development.get_site_mean_ae_dev
Get visit_med75.get_visit_med75
is orivisit classis_orivisit
is simaerep classis_simaerep
Calculate Max Rankmax_rank
create orivisit objectorivisit
Aggregate visit to patient level.pat_aggr
Create a study specific patient pool for samplingpat_pool
Plots AE per site as dots.plot_dots
Plot simulation example.plot_sim_example
Plot multiple simulation examples.plot_sim_examples
Plot ae development of study and sites highlighting at risk sites.plot_study
Plot patient visits against visit_med75.plot_visit_med75
plot AE under-reporting simulation resultsplot.simaerep
Poisson test for vector with site AEs vs vector with study AEs.poiss_test_site_ae_vs_study_ae
Prepare data for simulation.prep_for_sim
Calculate bootstrapped probability for obtaining a lower site mean AE number.prob_lower_site_ae_vs_study_ae
Execute a purrr or furrr function with a progress bar.purrr_bar
Start simulation after preparation.sim_after_prep
Calculate prob_lower for study sites using table operationssim_inframe
simulate single scenariosim_scenario
Calculate prob_lower and poisson.test pvalue for study sites.sim_sites
Simulate studies.sim_studies
simulate patient ae reporting test datasim_test_data_patient
Simulate Portfolio Test Datasim_test_data_portfolio
simulate study test datasim_test_data_study
simulate under-reportingsim_ur
Simulate Under-Reporting Scenariossim_ur_scenarios
Create simaerep objectsimaerep
Aggregate from visit to site level.site_aggr
Conditional 'with_progress'.with_progress_cnd