added "Aalen" "Johansen" to wordlist

R/aalen_johansen.R

@@ -83,18 +83,19 @@ aalen_johansen <- function(data,
     help$to <- ifelse(type2 != 2, "cens", type2 - 1)
     etmmm <- etm::etm(help, state_names, tra, "cens", s = 0)
     setmm <- summary(etmmm)[[2]]
-    ce_prob <- setmm[sum(setmm$time <= tau), ]$P
-    ce_prob_var <- setmm[sum(setmm$time <= tau), ]$var
+    trans_mat_tau <- setmm[sum(setmm$time <= tau), ]
+    ce_prob <- trans_mat_tau$P
+    ce_prob_var <- trans_mat_tau$var
   }
 
 
   if (c1 != 0 && c2 == 0) {
     help$to <- ifelse(type2 != 1, "cens", type2)
     etmmm <- etm::etm(help, state_names, tra, "cens", s = 0)
     setmm <- summary(etmmm)[[2]]
-
-    ae_prob <- setmm[sum(setmm$time <= tau), ]$P
-    ae_prob_var <- setmm[sum(setmm$time <= tau), ]$var
+    trans_mat_tau <- setmm[sum(setmm$time <= tau), ]
+    ae_prob <- trans_mat_tau$P
+    ae_prob_var <- trans_mat_tau$var
   }
 
   if (c1 != 0 && c2 != 0) {
@@ -106,11 +107,13 @@ aalen_johansen <- function(data,
     etmmm <- etm::etm(help, state_names, tra, "cens", s = 0)
     setmm <- summary(etmmm)
 
-    ae_prob <- setmm[[2]][sum(setmm[[2]]$time <= tau), ]$P
-    ae_prob_var <- setmm[[2]][sum(setmm[[2]]$time <= tau), ]$var
+    trans_mat_tau_ae <- setmm[[2]][sum(setmm[[2]]$time <= tau), ]
+    ae_prob <- trans_mat_tau_ae$P
+    ae_prob_var <- trans_mat_tau_ae$var
 
-    ce_prob <- setmm[[3]][sum(setmm[[3]]$time <= tau), ]$P
-    ce_prob_var <- setmm[[3]][sum(setmm[[3]]$time <= tau), ]$var
+    trans_mat_tau_ce <- setmm[[3]][sum(setmm[[3]]$time <= tau), ]
+    ce_prob <- trans_mat_tau_ce$P
+    ce_prob_var <- trans_mat_tau_ce$var
   }
 
 

tests/testthat/test-aalen_johansen.R

@@ -42,3 +42,20 @@ test_that("Aalen Johansen works without competing events", {
   expected <- c(ae_prob = 0.5897, ae_prob_var = 0.0404, ce_prob = 0, ce_prob_var = 0)
   expect_equal(result, expected, tolerance = 1e-4)
 })
+
+test_that("Aalen Johansen works without any events", {
+  set.seed(23)
+  df <- generate_data(
+    n = 25,
+    cens = c(0.2, 3),
+    haz_ae = 0.2,
+    haz_death = 0.3,
+    haz_soft = 0.5
+  )
+  df <- df[df$type_of_event != 1, ]
+  df <- df[df$type_of_event != 2, ]
+  df <- df[df$type_of_event != 3, ]
+  result <- aalen_johansen(data = df, ce = 2, tau = 4)
+  expected <- c(ae_prob = 0, ae_prob_var = 0, ce_prob = 0, ce_prob_var = 0)
+  expect_equal(result, expected, tolerance = 1e-4)
+})