## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, warning = FALSE, message = FALSE, comment = "#>" ) ## ----------------------------------------------------------------------------- library(CDMConnector) library(CohortSurvival) library(dplyr) library(cmprsk) library(survival) ## ----------------------------------------------------------------------------- cdm <- CohortSurvival::mockMGUS2cdm() ## ----fig.width=5-------------------------------------------------------------- input_survival_single <- cdm$mgus_diagnosis %>% addCohortSurvival( cdm = cdm, outcomeCohortTable = "death_cohort", outcomeCohortId = 1 ) input_survival_single %>% glimpse() ## ----------------------------------------------------------------------------- survival::coxph(survival::Surv(time, status) ~ age + sex, data = input_survival_single) survival::survdiff(survival::Surv(time, status) ~ sex, data = input_survival_single) ## ----------------------------------------------------------------------------- input_survival_cr <- cdm$mgus_diagnosis %>% addCompetingRiskCohortSurvival( cdm = cdm, outcomeCohortTable = "progression", outcomeCohortId = 1, competingOutcomeCohortTable = "death_cohort", competingOutcomeCohortId = 1 ) %>% glimpse() ## ----fig.height=6, fig.width=8------------------------------------------------ input_survival_cr <- input_survival_cr %>% dplyr::mutate(sex = dplyr::if_else(sex == "M", 0, 1)) covs <- data.frame(input_survival_cr$age, input_survival_cr$sex) names(covs) <- c("age", "sex") summary(cmprsk::crr(ftime = input_survival_cr$time, fstatus = input_survival_cr$status, cov1 = covs, failcode = 1, cencode = 0)) ## ----------------------------------------------------------------------------- cdmDisconnect(cdm)