Package: CohortSurvival 0.6.0

Edward Burn

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

CohortSurvival_0.6.0.tar.gz
CohortSurvival_0.6.0.tar.gz(r-4.5-noble)CohortSurvival_0.6.0.tar.gz(r-4.4-noble)
CohortSurvival_0.6.0.tgz(r-4.4-emscripten)CohortSurvival_0.6.0.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

4.20 score 15 scripts 327 downloads 25 exports 58 dependencies

Last updated 11 days agofrom:dfad9dfe37. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 11 2024
R-4.5-linux	OK	Nov 11 2024

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

Dependencies:backports bit bit64 blob broom CDMConnector checkmate cli clipr colorspace cpp11 crayon DBI dbplyr diffobj dplyr fansi farver fs generics glue hms jsonlite labeling lattice lifecycle lubridate magrittr Matrix munsell omopgenerics PatientProfiles pillar pkgconfig prettyunits progress purrr R6 RColorBrewer readr rlang scales snakecase stringi stringr survival tibble tidyr tidyselect timechange tzdb utf8 vctrs viridisLite visOmopResults vroom waldo withr

Competing risk survival

Rendered froma02_Competing_risk_survival.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-11-10
Started: 2023-12-08

Further survival analyses

Rendered froma03_Further_survival_analyses.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-11-10
Started: 2024-05-07

Single outcome event of interest

Rendered froma01_Single_event_of_interest.Rmdusingknitr::rmarkdownon Nov 11 2024.

Last update: 2024-11-10
Started: 2023-12-08

Citation

Readme and manuals

Help Manual

Help page	Topics
Add survival information to a cohort table	addCohortSurvival
Add competing risk survival information to a cohort table	addCompetingRiskCohortSurvival
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
To create a death cohort	generateDeathCohortSet
Create mock CDM reference with survival::mgus2 dataset	mockMGUS2cdm
Additional arguments for the function tableSurvival()	optionsTableSurvival
Plot survival results	plotSurvival
Table with survival summary	tableSurvival