(v1.4.0.9025) is_new_episode()

tests/testthat/test-first_isolate.R

@@ -204,11 +204,5 @@ test_that("first isolates work", {
   expect_true(all(example_isolates %pm>%
                     pm_distinct(mo, .keep_all = TRUE) %pm>%
                     first_isolate() == TRUE))
-  
-  library(dplyr)
-  # is_new_episode
-  old <- example_isolates %>% mutate(out = first_isolate(., include_unknown = TRUE))
-  new <- example_isolates %>% group_by(mo) %>% mutate(out = is_new_episode())
-  expect_identical(which(old$out), which(new$out))
 
 })

tests/testthat/test-is_new_episode.R

@@ -0,0 +1,55 @@
+# ==================================================================== #
+# TITLE                                                                #
+# Antimicrobial Resistance (AMR) Analysis for R                        #
+#                                                                      #
+# SOURCE                                                               #
+# https://github.com/msberends/AMR                                     #
+#                                                                      #
+# LICENCE                                                              #
+# (c) 2018-2020 Berends MS, Luz CF et al.                              #
+# Developed at the University of Groningen, the Netherlands, in        #
+# collaboration with non-profit organisations Certe Medical            #
+# Diagnostics & Advice, and University Medical Center Groningen.       # 
+#                                                                      #
+# This R package is free software; you can freely use and distribute   #
+# it for both personal and commercial purposes under the terms of the  #
+# GNU General Public License version 2.0 (GNU GPL-2), as published by  #
+# the Free Software Foundation.                                        #
+# We created this package for both routine data analysis and academic  #
+# research and it was publicly released in the hope that it will be    #
+# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY.              #
+#                                                                      #
+# Visit our website for the full manual and a complete tutorial about  #
+# how to conduct AMR analysis: https://msberends.github.io/AMR/        #
+# ==================================================================== #
+
+context("is_new_episode.R")
+
+test_that("new episodes work", {
+  skip_on_cran()
+  
+  test_df <- rbind(
+    data.frame(
+      date = as.Date(c("2015-01-01", "2015-10-01", "2016-02-04", "2016-12-31", "2017-01-01", "2017-02-01", "2017-02-05", "2020-01-01")),
+      patient_id = "A"
+    ),
+    data.frame(
+      date = as.Date(c("2015-01-01", "2016-02-01", "2016-12-31", "2017-01-01", "2017-02-03")),
+      patient_id = "B"
+    ))
+  
+  library(dplyr)
+  expect_identical(test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date)) %>% pull(f),
+                   c(TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE))
+  
+  suppressMessages(
+    x <- example_isolates %>%
+      mutate(out = first_isolate(., include_unknown = TRUE, info = FALSE))
+  )
+  
+  y <- example_isolates %>%
+    group_by(patient_id, mo) %>%
+    mutate(out = is_new_episode(date))
+  
+  expect_identical(which(x$out), which(y$out))
+})

tests/testthat/test-like.R

@@ -31,10 +31,7 @@ test_that("`like` works", {
   
   expect_true("test" %like% "test")
   expect_false("test" %like_case% "TEST")
-  
-  expect_false("test" %not_like% "test")
-  expect_true("test" %not_like_case% "TEST")
-  
+
   expect_true(as.factor("test") %like% "TEST")
   expect_identical(factor(c("Test case", "Something different", "Yet another thing")) %like% c("case", "diff", "yet"),
                    c(TRUE, TRUE, TRUE))