library(survival) survObject <- survfit(Surv(time, status) ~ sex, data = lung) # Test 1: Basic functionality - lot without error test_that("surv.plot can plot without error", { expect_silent(surv.plot(fit = survObject)) }) # Test 2: Invalid `y.unit` parameter should throw error test_that("surv.plot throws error for invalid y.unit parameter", { expect_error(surv.plot(fit = survObject, time.unit = "month", y.unit = "invalid"), "'invalid' is not a valid argument for `y.unit`!") }) # Test 3: Invalid `theme` parameter should throw error test_that("surv.plot throws error for invalid theme parameter", { expect_error(surv.plot(fit = survObject, reference.arm = "1", time.unit = "month", theme = "invalid"), "Provided theme argument does not exist!") }) # Test 4: Invalid `risktable` parameter should throw error test_that("surv.plot throws error for invalid risktable parameter", { expect_error(surv.plot(fit =survObject, reference.arm = "1", time.unit = "month", risktable = "invalid"), "`risktable` expecting TRUE or FALSE as an argument!") }) ## Test 5: Custom colour assignment should not raise errors test_that("surv.plot handles default color assignment", { expect_silent(surv.plot(fit = survObject, reference.arm = "1", time.unit = "month", col = c("#E41A1C", "#4DAF4A", "#377EB8"))) }) # Test 6: Ensure survival plot handles empty survival object gracefully test_that("Plotting an empty survival object should raise an error", { expect_error(surv.plot(fit = survfit(Surv() ~ 1, data = NULL))) }) # Test 7: Verify that setting an incorrect reference arm raises error test_that("Setting an incorrect reference arm should raise an error.", { expect_error(surv.plot(fit = survObject,reference.arm = "3")) }) # Test 8: Verify that statistics is given in % test_that("Convert y unit into percent.",{ expect_silent(surv.plot(fit = survObject, y.unit = "percent")) }) test_that("Convert y unit into percent and check label",{ expect_silent(surv.plot(fit = survObject, y.unit = "percent", segment.quantile = 0.5, time.unit = "day")) }) # Test 9: Ensure survival plot can handle quantiles and timepoints test_that("Ensure `segment.quanitle` is handles without error.",{ expect_silent(surv.plot(fit = survObject, segment.quantile = 0.5, segment.type = 1)) }) test_that("Ensure `segment.quanitle` is handles without error.",{ expect_silent(surv.plot(fit = survObject, segment.quantile = 0.5, segment.type = 2)) }) test_that("Ensure `segment.quanitle` is handles without error.",{ expect_silent(surv.plot(fit = survObject, segment.quantile = 0.5, segment.type = 3)) }) test_that("Ensure `segment.timpoint` is handles without error.",{ expect_silent(surv.plot(fit = survObject, segment.timepoint = 360, segment.type = 1)) }) test_that("Ensure `segment.timpoint` is handles without error.",{ expect_silent(surv.plot(fit = survObject, segment.timepoint = 360, segment.type = 2)) }) test_that("Ensure `segment.timpoint` is handles without error.",{ expect_silent(surv.plot(fit = survObject, segment.timepoint = 360, segment.type = 3)) }) # Test 10: Check `segment.annotation` parameters test_that("surv.plot throws error for invalid risktable parameter", { expect_error(surv.plot(fit =survObject, segment.annotation = "invalid")) }) test_that("surv.plot throws error for invalid risktable parameter", { expect_silent(surv.plot(fit =survObject, segment.timepoint = 0.5 , segment.annotation = c(300, 0.125))) }) test_that("surv.plot throws error for invalid risktable parameter", { expect_silent(surv.plot(fit =survObject, segment.timepoint = 0.5 , segment.annotation = "left")) }) test_that("surv.plot throws error for invalid risktable parameter", { expect_silent(surv.plot(fit =survfit(Surv(time, status) ~ 1, data = lung), segment.timepoint = 0.5 , segment.annotation = "top")) }) test_that("surv.plot throws error for invalid risktable parameter", { expect_silent(surv.plot(fit =survfit(Surv(time, status) ~ sex, data = lung), segment.timepoint = 0.5 , segment.annotation = "top")) }) test_that("surv.plot throws error for invalid risktable parameter", { expect_silent(surv.plot(fit =survfit(Surv(time, status) ~ sex, data = lung), segment.timepoint = 0.5 , segment.annotation = "bottomleft")) }) test_that("surv.plot throws error for invalid risktable parameter", { expect_silent(surv.plot(fit =survfit(Surv(time, status) ~ 1, data = lung), segment.timepoint = 0.5 , segment.annotation = "none")) }) # Test 11: Test risktable test_that("Check if risktable colour can be modified", { expect_silent(surv.plot(fit =survObject, risktable.col = c("red", "yellow"))) }) test_that("Ensure that legend can handle invalid argument", { expect_error(surv.plot(fit =survObject, legend = "invalid")) }) test_that("Ensure that legend can be modified manually", { expect_silent(surv.plot(fit =survObject, legend.name = "legend")) }) # Test 12: Test Statistics test_that("Check logrank statistics", { expect_silent(surv.plot(fit =survObject, stat = "logrank")) }) test_that("Check coxph statistics", { expect_silent(surv.plot(fit =survObject, stat = "coxph", stat.position = "bottomleft")) }) test_that("Check coxph_logrank statistics", { expect_silent(surv.plot(fit =survObject, stat = "coxph_logrank", stat.position = "topright")) }) test_that("Check coxph_logrank statistics", { expect_silent(surv.plot(fit =survObject, stat = "coxph_logrank", stat.position = c(170, 0.5))) }) # Test 13: Test pre defined themes test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), theme = "ESMO")) }) test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), theme = "ESMO")) }) test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), theme = "ESMO", risktable = FALSE)) }) test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), theme = "SAKK", risktable = FALSE)) }) test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), theme = "SAKK", risktable = FALSE)) }) test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), theme = "Lancet")) }) test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), theme = "Lancet")) }) test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), theme = "JCO")) }) test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), theme = "JCO")) }) test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), theme = "WCLC")) }) test_that("Check if defined theme is executed", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), theme = "WCLC")) }) # Test 14: Test grid test_that("Setting an invalid grid argument.", { expect_error(surv.plot(fit = survObject, grid = "invalid")) }) test_that("Setting an invalid grid argument.", { expect_silent(surv.plot(fit = survObject, grid = TRUE)) }) # Test 15: Test statistics for one arm test_that("Setting an invalid stats argument.", { expect_error(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), stat = "coxph")) }) # Test 16: Check risktable.title test_that("Check if risktable.title gives a valid output.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), risktable.censoring = TRUE)) }) test_that("Check if risktable.title gives a valid output.", { expect_error(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), risktable.censoring = "invalid")) }) # Test 17: Check confidence band colour test_that("Check if conf.band.col gives a valid output.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), conf.band.col = NULL)) }) # Test 18: Invalid `time.unit` parameter should throw error rest not test_that("Ensure `time.unit` is handles without error.", { expect_error(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), time.unit = "invalid")) }) test_that("Check if conf.band.col gives a valid output.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), time.unit = "day")) }) test_that("Check if conf.band.col gives a valid output.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), time.unit = "year")) }) # Test 19: Check for short annotation test_that("Check if short annotation works without an error.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), segment.quantile = 0.5, segment.confint = FALSE)) }) test_that("Check if short annotation works without an error.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), segment.quantile = 0.5, segment.confint = FALSE, time.unit = "day")) }) test_that("Check if short annotation works without an error.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), segment.quantile = 0.25, segment.confint = FALSE)) }) test_that("Check if short annotation can handle error.", { expect_error(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.quantile = 0.25, segment.confint = FALSE)) }) test_that("Check for annotation with only one arm.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.annotation.two.lines = FALSE, segment.quantile = 0.50)) }) test_that("Check for annotation with only one arm.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.annotation.two.lines = FALSE, segment.quantile = 0.25, segment.main = "Quantile")) }) test_that("Check for annotation with only one arm.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), segment.timepoint = 360, segment.confint = FALSE)) }) test_that("Check for annotation with only one arm.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), segment.timepoint = 360, segment.confint = FALSE, y.unit = "percent")) }) test_that("Check for annotation with only one arm.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), segment.quantile = 0.25, segment.confint = TRUE, y.unit = "percent")) }) test_that("Check for annotation with only one arm.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.annotation.two.lines = FALSE, segment.main = "Segment Title", segment.quantile = 0.50)) }) test_that("Check for annotation with only one arm.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.annotation.two.lines = TRUE, segment.quantile = 0.50)) }) test_that("Check for annotation with only one arm.", { expect_silent(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.annotation.two.lines = TRUE, segment.quantile = 0.50, y.unit = "percent")) }) # Test 20: Check Error of segment test_that("Check if segment can handle error.", { expect_error(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.quantile = 0.50, segment.timepoint = 360)) }) # Test 21: Check Error message if no confidence interval should be displayed but number of arms is not equal to 2 test_that("Check if CI with one arm can handle error.", { expect_error(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.quantile = 0.50, segment.confint = FALSE)) }) # Test 22: test_that("Check if error with different segment type can handle error.", { expect_error(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.quantile = 0.50, segment.timepoint = 360, segment.type = 1)) }) test_that("Check if error with different segment type can handle error.", { expect_error(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.quantile = 0.50, segment.timepoint = 360, segment.type = 2)) }) test_that("Check if error with different segment type can handle error.", { expect_error(surv.plot(fit = survfit(Surv(time, status) ~ 1, data = lung), segment.quantile = 0.50, segment.timepoint = 360, segment.type = 3)) }) # Test 23: Check Warning message if segment at several time points or quantiles should be added and segment.main is not null test_that("Check if error with different segment type can handle error.", { expect_warning(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), segment.quantile = c(0.25, 0.5), segment.main = "Test")) }) test_that("Check if error with different segment type can handle error.", { expect_warning(surv.plot(fit = survfit(Surv(time, status) ~ sex, data = lung), segment.timepoint = c(300, 650), segment.main = "Test")) })