This package is considered a duplicate. The official version of this package is found at:https://openpharma.r-universe.dev/simaerep

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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simaerep.pdf |simaerep.html✨
simaerep/json (API)
NEWS

# Install 'simaerep' in R:

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

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

Pkgdown:https://openpharma.github.io

On CRAN:

ae-reporting clinical-trials

5.20 score 21 stars 25 scripts 217 downloads 38 exports 54 dependencies

Last updated 3 months agofrom:fa10836cd0. Checks:OK: 7. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Dec 01 2024
R-4.5-win	OK	Dec 01 2024
R-4.5-linux	OK	Dec 01 2024
R-4.4-win	OK	Dec 01 2024
R-4.4-mac	OK	Dec 01 2024
R-4.3-win	OK	Dec 01 2024
R-4.3-mac	OK	Dec 01 2024

Exports:%>%aggr_duplicated_visits check_df_visit eval_sites exp_implicit_missing_visits get_config get_ecd_values get_pat_pool_config get_portf_perf is_orivisit is_simaerep max_rank orivisit pat_aggr pat_pool plot_dots plot_sim_example plot_sim_examples plot_study plot_visit_med75 poiss_test_site_ae_vs_study_ae prep_for_sim prob_lower_site_ae_vs_study_ae purrr_bar sim_after_prep sim_inframe sim_scenario sim_sites sim_studies sim_test_data_patient sim_test_data_portfolio sim_test_data_study sim_ur sim_ur_scenarios simaerep simaerep_inframe site_aggr with_progress_cnd

Dependencies:blob cli codetools colorspace cowplot cpp11 DBI dbplyr digest dplyr evaluate fansi farver forcats furrr future generics ggplot2 globals glue gtable highr isoband knitr labeling lattice lifecycle listenv magrittr MASS Matrix mgcv munsell nlme parallelly pillar pkgconfig progressr purrr R6 RColorBrewer rlang scales stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr xfun yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
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 Configuration	get_config
Get empirical cumulative distribution values of pval or prob_lower	get_ecd_values
Configure study patient pool by site parameters.	get_pat_pool_config
Get Portfolio Performance	get_portf_perf
Get site mean ae development.	get_site_mean_ae_dev
Get visit_med75.	get_visit_med75
is orivisit class	is_orivisit
is simaerep class	is_simaerep
Calculate Max Rank	max_rank
create orivisit object	orivisit
Aggregate visit to patient level.	pat_aggr
Create a study specific patient pool for sampling	pat_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 results	plot.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 operations	sim_inframe
simulate single scenario	sim_scenario
Calculate prob_lower and poisson.test pvalue for study sites.	sim_sites
Simulate studies.	sim_studies
simulate patient ae reporting test data	sim_test_data_patient
Simulate Portfolio Test Data	sim_test_data_portfolio
simulate study test data	sim_test_data_study
simulate under-reporting	sim_ur
Simulate Under-Reporting Scenarios	sim_ur_scenarios
Create simaerep object	simaerep
Aggregate from visit to site level.	site_aggr
Conditional 'with_progress'.	with_progress_cnd