fix

R/find_parameters_other.R

@@ -246,7 +246,7 @@ find_parameters.deltaMethod <- function(x, flatten = FALSE, ...) {
 
 
 #' @export
-find_parameters.coxph <- function(x, verbose = TRUE, ...) {
+find_parameters.coxph <- function(x, flatten = FALSE, ...) {
   cf <- stats::coef(summary(x))
   out <- list(conditional = rownames(cf))
 

tests/testthat/test-coxph-panel.R

@@ -1,163 +1,100 @@
 skip_if_not_installed("survival")
 skip_if_not_installed("withr")
 
+lung <- survival::lung
+Surv <- survival::Surv
+
 mod <- survival::coxph(
   Surv(time, status) ~ ph.ecog + tt(age),
   data = lung,
-  tt = function(x, t, ...) pspline(x + t / 365.25)
+  tt = function(x, t, ...) survival::pspline(x + t / 365.25)
 )
 
 test_that("model_info", {
-  expect_true(model_info(m1)$is_logit)
-  expect_false(model_info(m1)$is_linear)
+  expect_true(model_info(mod)$is_logit)
+  expect_false(model_info(mod)$is_linear)
 })
 
 test_that("find_predictors", {
-  expect_identical(find_predictors(m1), list(conditional = c("sex", "age", "ph.ecog")))
-  expect_null(find_predictors(m1, effects = "random"))
+  expect_identical(find_predictors(mod), list(conditional = c( "ph.ecog", "age")))
+  expect_null(find_predictors(mod, effects = "random"))
 })
 
 test_that("find_response", {
-  expect_identical(find_response(m1), "Surv(time, status)")
-  expect_identical(find_response(m1, combine = FALSE), c("time", "status"))
+  expect_identical(find_response(mod), "Surv(time, status)")
+  expect_identical(find_response(mod, combine = FALSE), c("time", "status"))
 })
 
 test_that("link_inverse", {
-  expect_equal(link_inverse(m1)(0.2), plogis(0.2), tolerance = 1e-5)
+  expect_equal(link_inverse(mod)(0.2), plogis(0.2), tolerance = 1e-5)
 })
 
 test_that("get_data", {
   ## NOTE check back every now and then and see if tests still work
   skip("works interactively")
-  expect_s3_class(get_data(m1), "data.frame")
-  expect_identical(dim(get_data(m1)), c(166L, 10L))
+  expect_s3_class(get_data(mod), "data.frame")
+  expect_identical(dim(get_data(mod)), c(227L, 4L))
 })
 
 
-withr::with_environment(
-  new.env(),
-  test_that("get_data: regression test for previous bug", {
-    dat_regression_test <- data.frame(
-      time = c(4, 3, 1, 1, 2, 2, 3),
-      status = c(1, 1, 1, 0, 1, 1, 0),
-      x = c(0, 2, 1, 1, 1, 0, 0),
-      sex = c(0, 0, 0, 0, 1, 1, 1)
-    )
-    mod <- survival::coxph(Surv(time, status) ~ x + strata(sex),
-      data = dat_regression_test,
-      ties = "breslow"
-    )
-    expect_equal(get_data(mod), dat_regression_test, ignore_attr = TRUE)
-  })
-)
-
-
-withr::with_environment(
-  new.env(),
-  test_that("get_data: regression test for data stored as list", {
-    dat_regression_test <- list(
-      time = c(4, 3, 1, 1, 2, 2, 3),
-      status = c(1, 1, 1, 0, 1, 1, 0),
-      x = c(0, 2, 1, 1, 1, 0, 0),
-      sex = c(0, 0, 0, 0, 1, 1, 1)
-    )
-    mod <- survival::coxph(Surv(time, status) ~ x + strata(sex),
-      data = dat_regression_test,
-      ties = "breslow"
-    )
-    expect_equal(get_data(mod), as.data.frame(dat_regression_test), ignore_attr = TRUE)
-  })
-)
-
-
 test_that("find_formula", {
-  expect_length(find_formula(m1), 1)
+  expect_length(find_formula(mod), 1)
   expect_equal(
-    find_formula(m1),
-    list(conditional = as.formula(
-      "Surv(time, status) ~ sex + age + ph.ecog"
-    )),
+    find_formula(mod),
+    list(conditional = as.formula("Surv(time, status) ~ ph.ecog + tt(age)")),
     ignore_attr = TRUE
   )
 })
 
 test_that("find_variables", {
-  expect_identical(find_variables(m1), list(
+  expect_identical(find_variables(mod), list(
     response = c("time", "status"),
-    conditional = c("sex", "age", "ph.ecog")
+    conditional = c( "ph.ecog", "age")
   ))
+
   expect_identical(
-    find_variables(m1, flatten = TRUE),
-    c("time", "status", "sex", "age", "ph.ecog")
+    find_variables(mod, flatten = TRUE),
+    c("time", "status", "ph.ecog", "age")
   )
 })
 
 test_that("n_obs", {
-  expect_identical(n_obs(m1), 226L)
+  expect_identical(n_obs(mod), 227L)
 })
 
 test_that("linkfun", {
-  expect_false(is.null(link_function(m1)))
+  expect_false(is.null(link_function(mod)))
 })
 
 test_that("is_multivariate", {
-  expect_false(is_multivariate(m1))
+  expect_false(is_multivariate(mod))
 })
 
-test_that("find_parameters", {
-  expect_identical(
-    find_parameters(m1),
-    list(
-      conditional = c("sexfemale", "age", "ph.ecogok", "ph.ecoglimited")
+withr::with_package(
+  "survival",
+  test_that("find_parameters", {
+    expect_identical(
+      find_parameters(mod),
+      list(conditional = c("ph.ecog", "tt(age), linear", "tt(age), nonlin"))
     )
-  )
-  expect_identical(nrow(get_parameters(m1)), 4L)
-  expect_identical(
-    get_parameters(m1)$Parameter,
-    c("sexfemale", "age", "ph.ecogok", "ph.ecoglimited")
-  )
-})
+    expect_identical(nrow(get_parameters(mod)), 4L)
+    expect_identical(
+      get_parameters(mod)$Parameter,
+      c("ph.ecog", "tt(age), linear", "tt(age), nonlin")
+    )
+  })
+)
 
 test_that("find_terms", {
   expect_identical(
-    find_terms(m1),
+    find_terms(mod),
     list(
       response = "Surv(time, status)",
-      conditional = c("sex", "age", "ph.ecog")
+      conditional = c( "ph.ecog", "tt(age)")
     )
   )
 })
 
 test_that("find_statistic", {
-  expect_identical(find_statistic(m1), "z-statistic")
-})
-
-test_that("JM", {
-  data("aids", package = "JM")
-  m <- survival::coxph(Surv(start, stop, event) ~ CD4, data = aids)
-  d <- get_data(m)
-  expect_identical(dim(d), c(1405L, 4L))
-  expect_named(d, c("start", "stop", "event", "CD4"))
-  expect_identical(find_variables(m), list(response = c("start", "stop", "event"), conditional = "CD4"))
-})
-
-test_that("get_statistic", {
-  skip_if_not_installed("survival")
-  bladder1 <- bladder[bladder$enum < 5, ]
-  mod <- survival::coxph(
-    Surv(stop, event) ~ (rx + size + number) * strata(enum),
-    cluster = id, bladder1, robust = TRUE
-  )
-  z1 <- get_statistic(mod)$Statistic
-  z2 <- coef(summary(mod))[, "z"]
-  expect_equal(z1, z2, ignore_attr = TRUE)
-
-  lung <- survival::lung
-  mod <- survival::coxph(
-    formula = Surv(time, status) ~ age + sex + survival::frailty(inst),
-    data = lung
-  )
-  z1 <- get_statistic(mod)$Statistic
-  z2 <- coef(summary(mod))[, "Chisq"]
-  expect_equal(z1, z2, ignore_attr = TRUE)
+  expect_identical(find_statistic(mod), "chi-squared statistic")
 })