Merge branch 'master' of https://gitlab.com/msberends/AMR

codecov.yml

@@ -1,6 +1,6 @@
 codecov:
   notify:
-    require_ci_to_pass: no
+    require_ci_to_pass: no # allow fail
   ci:
     - !appveyor # ignore CI builds by AppVeyor
 
@@ -18,3 +18,4 @@ coverage:
 ignore:
   - "R/atc_online.R"
   - "R/mo_source.R"
+  - "R/resistance_predict.R"

tests/testthat/test-resistance_predict.R

@@ -19,18 +19,18 @@
 # Visit our website for more info: https://msberends.gitlab.io/AMR.    #
 # ==================================================================== #
 
-context("portion.R")
+context("resistance_predict.R")
 
 test_that("prediction of rsi works", {
-  # AMX_R <- septic_patients %>%
+  AMX_R <- septic_patients %>%
-  #   filter(mo == "B_ESCHR_COL") %>%
+    filter(mo == "B_ESCHR_COL") %>%
-  #   rsi_predict(col_ab = "AMX",
+    rsi_predict(col_ab = "AMX",
-  #               col_date = "date",
+                col_date = "date",
-  #               minimum = 10,
+                minimum = 10,
-  #               info = TRUE) %>%
+                info = TRUE) %>%
-  #   pull("value")
+    pull("value")
-  # # AMX resistance will increase according to data set `septic_patients`
+  # AMX resistance will increase according to data set `septic_patients`
-  # expect_true(AMX_R[3] < AMX_R[20])
+  expect_true(AMX_R[3] < AMX_R[20])
 
   x <- resistance_predict(septic_patients, col_ab = "AMX", year_min = 2010)
   plot(x)