test_that("basic Survival plot", { skip_on_cran() cdm <- mockMGUS2cdm() surv <- estimateSingleEventSurvival(cdm, targetCohortTable = "mgus_diagnosis", targetCohortId = 1, outcomeCohortTable = "death_cohort", outcomeCohortId = 1 ) plot <- plotSurvival(surv) expect_true(ggplot2::is.ggplot(plot)) CDMConnector::cdmDisconnect(cdm) }) test_that("plot facets and colour", { skip_on_cran() cdm <- mockMGUS2cdm() surv <- estimateSingleEventSurvival(cdm, targetCohortTable = "mgus_diagnosis", targetCohortId = 1, outcomeCohortTable = "death_cohort", outcomeCohortId = 1, strata=list(c("sex", "age_group")) ) plot <- plotSurvival(surv, facet = "sex", colour = "age_group") expect_true(ggplot2::is.ggplot(plot)) plot <- plotSurvival(surv, facet = c("sex","age_group"), colour = "cdm_name") expect_true(ggplot2::is.ggplot(plot)) plot <- plotSurvival(surv, facet = "sex", colour = "age_group") expect_true(ggplot2::is.ggplot(plot)) CDMConnector::cdmDisconnect(cdm) }) test_that("basic cumulative incidence plot", { skip_on_cran() cdm <- mockMGUS2cdm() surv <- estimateSingleEventSurvival(cdm, targetCohortTable = "mgus_diagnosis", targetCohortId = 1, outcomeCohortTable = "death_cohort", outcomeCohortId = 1 ) plot <- plotSurvival(surv, cumulativeFailure = TRUE) expect_true(ggplot2::is.ggplot(plot)) survCR <- estimateCompetingRiskSurvival(cdm, targetCohortTable = "mgus_diagnosis", outcomeCohortTable = "progression", competingOutcomeCohortTable = "death_cohort" ) plot <- plotSurvival(survCR, cumulativeFailure = TRUE, colour = "variable") expect_true(ggplot2::is.ggplot(plot)) # cumulativeFailure must be true when working with competing risk result expect_error(plotSurvival(survCR, xscale = "years", cumulativeFailure = FALSE, colour = "variable")) CDMConnector::cdmDisconnect(cdm) }) test_that("plot risk tables", { skip_on_cran() cdm <- mockMGUS2cdm() surv <- estimateSingleEventSurvival(cdm, targetCohortTable = "mgus_diagnosis", targetCohortId = 1, outcomeCohortTable = "death_cohort", outcomeCohortId = 1, strata=list(c("sex", "age_group")) ) plot <- plotSurvival(surv, facet = "sex", colour = "age_group", riskTable = TRUE) expect_true(ggplot2::is.ggplot(plot)) plot <- plotSurvival(surv, colour = c("age_group", "sex"), riskTable = TRUE) expect_true(ggplot2::is.ggplot(plot)) surv <- estimateSingleEventSurvival(cdm, targetCohortTable = "mgus_diagnosis", targetCohortId = 1, outcomeCohortTable = "death_cohort", outcomeCohortId = 1) plot <- plotSurvival(surv, riskTable = TRUE, riskInterval = 10) expect_true(ggplot2::is.ggplot(plot)) CDMConnector::cdmDisconnect(cdm) }) test_that("empty plot", { skip_on_cran() cdm <- mockMGUS2cdm() surv <- omopgenerics::emptySummarisedResult() plotSurvival(surv) CDMConnector::cdmDisconnect(cdm) })