sf1 <- survfit2(Surv(time, status) ~ 1, data = df_lung) sf2 <- survfit2(Surv(time, status) ~ sex, data = df_lung) sf3 <- survfit2(Surv(time, status) ~ sex + ph.ecog, data = df_lung) test_that("ggsurvfit() works", { expect_error( lst_survfit2 <- list(sf1, sf2, sf3) %>% lapply(ggsurvfit), NA ) vdiffr::expect_doppelganger("sf1-ggsurvfit", lst_survfit2[[1]]) vdiffr::expect_doppelganger("sf2-ggsurvfit", lst_survfit2[[2]]) vdiffr::expect_doppelganger("sf3-ggsurvfit", lst_survfit2[[3]]) expect_error( lst_survfit2_risk <- list(sf1, sf2, sf3) %>% lapply(function(x) ggsurvfit(x, type = "risk")), NA ) vdiffr::expect_doppelganger("sf1-ggsurvfit_risk", lst_survfit2_risk[[1]]) vdiffr::expect_doppelganger("sf2-ggsurvfit_risk", lst_survfit2_risk[[2]]) vdiffr::expect_doppelganger("sf3-ggsurvfit_risk", lst_survfit2_risk[[3]]) expect_error( lst_survfit2_cumhaz <- list(sf1, sf2, sf3) %>% lapply(function(x) ggsurvfit(x, type = "cumhaz")), NA ) vdiffr::expect_doppelganger("sf1-ggsurvfit_cumhaz", lst_survfit2_cumhaz[[1]]) vdiffr::expect_doppelganger("sf2-ggsurvfit_cumhaz", lst_survfit2_cumhaz[[2]]) vdiffr::expect_doppelganger("sf3-ggsurvfit_cumhaz", lst_survfit2_cumhaz[[3]]) expect_error( lst_survfit2_custom <- list(sf1, sf2, sf3) %>% lapply(function(x) ggsurvfit(x, type = function(x) 1 - x)), NA ) vdiffr::expect_doppelganger("sf1-ggsurvfit_custom", lst_survfit2_custom[[1]]) vdiffr::expect_doppelganger("sf2-ggsurvfit_custom", lst_survfit2_custom[[2]]) vdiffr::expect_doppelganger("sf3-ggsurvfit_custom", lst_survfit2_custom[[3]]) expect_error( lst_survfit2_linetype <- list(sf2, sf3) %>% lapply(ggsurvfit, linetype_aes = TRUE), NA ) vdiffr::expect_doppelganger("sf2-ggsurvfit_linetype", lst_survfit2_linetype[[1]]) vdiffr::expect_doppelganger("sf3-ggsurvfit_linetype", lst_survfit2_linetype[[2]]) expect_error( lst_survfit_KMunicate <- list(sf1, sf2, sf3) %>% lapply(function(x) ggsurvfit(x, theme = theme_ggsurvfit_KMunicate())), NA ) vdiffr::expect_doppelganger("sf1-ggsurvfit-KMunicate", lst_survfit_KMunicate[[1]]) vdiffr::expect_doppelganger("sf2-ggsurvfit-KMunicate", lst_survfit_KMunicate[[2]]) vdiffr::expect_doppelganger("sf3-ggsurvfit-KMunicate", lst_survfit_KMunicate[[3]]) # test that the variable names are stripped when using transformations vdiffr::expect_doppelganger( "sf2-ggsurvfit-strata-transformation", survfit2(Surv(time, status) ~ as.numeric(sex), df_lung) %>% ggsurvfit() ) # test the default ADTTE x-axis label comes from PARAM column expect_equal( ggsurvfit(survfit2(Surv_CNSR() ~ 1, data = adtte)) %>% ggplot2::ggplot_build() %>% `[[`("plot") %>% `[[`("labels") %>% `[[`("x"), adtte[["PARAM"]] %>% unique() ) # testing the default label when using Surv_CNSR() without a PARAM COLUMN expect_equal( survfit2( Surv_CNSR() ~ STR01L, data = adtte %>% dplyr::select(-c(PARAM, PARAMCD)) ) %>% .default_x_axis_label(), "Time" ) # check ADTTE PARAM usage expect_warning( adtte %>% dplyr::mutate( PARAMCD = rep_len(c("PFS", "OS"), length.out = dplyr::n()) ) %>% dplyr::select(-PARAM) %>% survfit2(Surv_CNSR() ~ 1, data = .), "usage is likely incorrect" ) expect_warning( adtte %>% dplyr::mutate( PARAMCD = rep_len(c("PFS", "OS"), length.out = dplyr::n()) ) %>% dplyr::select(-PARAM) %>% survfit2(Surv_CNSR() ~ PARAMCD, data = .), NA ) df_param2 <- adtte %>% dplyr::mutate(PARAM = rep_len(c("PFS", "OS"), length.out = dplyr::n())) expect_warning( survfit2(Surv_CNSR() ~ 1, data = df_param2), "usage is likely incorrect" ) # PARAM will not be used as label because of incorrect usage expect_equal( suppressWarnings(survfit2(Surv_CNSR() ~ 1, data = df_param2)) %>% ggsurvfit() %>% ggplot2::ggplot_build() %>% `[[`("plot") %>% `[[`("labels") %>% `[[`("x"), "Time" ) # x-axis label comes from PARAM expect_equal( survfit2(Surv_CNSR() ~ PARAM, data = df_param2) %>% ggsurvfit() %>% ggplot2::ggplot_build() %>% `[[`("plot") %>% `[[`("labels") %>% `[[`("x"), "Time" ) expect_error(ggsurvfit(mtcars)) expect_error(survfit2(Surv(ttdeath, death_cr) ~ trt, tidycmprsk::trial) %>% ggsurvfit()) }) test_that("ggsurvfit() works with geoms with new data", { expect_error( p1 <- survfit2(Surv(time, status) ~ sex, data = df_lung) %>% ggsurvfit() + geom_point( data = mtcars, aes(y = mpg / max(mpg), x = hp / max(hp) * 30) ) + add_censor_mark() + add_quantile() + add_pvalue() + add_confidence_interval() + add_risktable(risktable_group = "risktable_stats") + add_risktable_strata_symbol() + add_legend_title(), NA ) expect_error( p2 <- survfit2(Surv(time, status) ~ sex, data = df_lung) %>% ggsurvfit() + add_censor_mark() + add_quantile() + add_pvalue() + add_confidence_interval() + add_risktable(risktable_group = "risktable_stats") + add_risktable_strata_symbol() + add_legend_title() + geom_point( data = mtcars, aes(y = mpg / max(mpg), x = hp / max(hp) * 30) ), NA ) # only check on mac skip_on_ci() vdiffr::expect_doppelganger("sf2-ggsurvfit_new_data_geom1", p1) vdiffr::expect_doppelganger("sf2-ggsurvfit_new_data_geom2", p2) })