Package: CohortSurvival 1.0.0

Kim López-Güell

CohortSurvival: Estimate Survival from Common Data Model Cohorts

Estimate survival using data mapped to the Observational Medical Outcomes Partnership common data model. Survival can be estimated based on user-defined study cohorts.

Authors:Kim López-Güell [aut, cre], Edward Burn [aut], Marti Catala [aut], Xintong Li [aut], Danielle Newby [aut], Nuria Mercade-Besora [aut]

CohortSurvival_1.0.0.tar.gz
CohortSurvival_1.0.0.tar.gz(r-4.5-noble)CohortSurvival_1.0.0.tar.gz(r-4.4-noble)
CohortSurvival_1.0.0.tgz(r-4.4-emscripten)CohortSurvival_1.0.0.tgz(r-4.3-emscripten)
CohortSurvival.pdf |CohortSurvival.html✨
CohortSurvival/json (API)

# Install 'CohortSurvival' in R:

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

Bug tracker:https://github.com/darwin-eu-dev/cohortsurvival/issues

Pkgdown site:https://darwin-eu-dev.github.io

On CRAN:

4.08 score 1000 downloads 24 exports 46 dependencies

Last updated 5 days agofrom:117bc57c19. Checks:3 OK. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 19 2025
R-4.5-linux	OK	Mar 19 2025
R-4.4-linux	OK	Mar 19 2025

Exports::=.data %>%addCohortSurvival as_label as_name asSurvivalResult attrition bind cohortCodelist cohortCount enquo enquos estimateCompetingRiskSurvival estimateSingleEventSurvival exportSummarisedResult importSummarisedResult mockMGUS2cdm optionsTableSurvival plotSurvival riskTable settings suppress tableSurvival

Dependencies:backports bit bit64 blob broom CDMConnector checkmate cli clipr clock cpp11 crayon DBI dbplyr dplyr fansi generics glue hms jsonlite lattice lifecycle magrittr Matrix omopgenerics PatientProfiles pillar pkgconfig prettyunits progress purrr R6 readr rlang snakecase stringi stringr survival tibble tidyr tidyselect tzdb utf8 vctrs vroom withr

Competing risk survival

Rendered froma02_Competing_risk_survival.Rmdusingknitr::rmarkdownon Mar 19 2025.

Last update: 2025-03-19
Started: 2023-12-08

Further survival analyses

Rendered froma03_Further_survival_analyses.Rmdusingknitr::rmarkdownon Mar 19 2025.

Last update: 2025-03-19
Started: 2024-05-07

Single outcome event of interest

Rendered froma01_Single_event_of_interest.Rmdusingknitr::rmarkdownon Mar 19 2025.

Last update: 2025-03-19
Started: 2023-12-08

Citation

Readme and manuals

Help Manual

Help page	Topics
Add survival information to a cohort table	addCohortSurvival
A tidy implementation of the summarised_characteristics object.	asSurvivalResult
Estimate survival for a given event and competing risk of interest using cohorts in the OMOP Common Data Model	estimateCompetingRiskSurvival
Estimate survival for a given event of interest using cohorts in the OMOP Common Data Model	estimateSingleEventSurvival
Create mock CDM reference with survival::mgus2 dataset	mockMGUS2cdm
Additional arguments for the function tableSurvival()	optionsTableSurvival
Plot survival results	plotSurvival
Table with survival events	riskTable
Table with survival summary	tableSurvival