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dplyr 0.8.0 support, fixes #7

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dr. M.S. (Matthijs) Berends
2018-12-22 22:39:34 +01:00
parent b937662a97
commit 0b8084871d
29 changed files with 555 additions and 479 deletions
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31
tests/testthat/test-first_isolate.R
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@ -19,7 +19,7 @@
context("first_isolate.R")
test_that("first isolates work", {
# septic_patients contains 1331 out of 2000 first isolates
# septic_patients contains 1315 out of 2000 first isolates
expect_equal(
sum(
first_isolate(tbl = septic_patients,
@ -139,16 +139,15 @@ test_that("first isolates work", {
mutate(first = first_isolate(., "date", "patient_id",
col_mo = "mo",
col_specimen = "specimen",
filter_specimen = "something_unexisting",
output_logical = FALSE)))
filter_specimen = "something_unexisting")))
# printing of exclusion message
expect_output(septic_patients %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id",
col_testcode = "gender",
testcodes_exclude = "M"))
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id",
col_testcode = "gender",
testcodes_exclude = "M"))
# errors
expect_error(first_isolate("date", "patient_id", col_mo = "mo"))
@ -158,18 +157,16 @@ test_that("first isolates work", {
# look for columns itself
expect_message(first_isolate(septic_patients))
expect_message(first_isolate(septic_patients %>%
mutate(mo = as.character(mo)) %>%
left_join_microorganisms(),
col_genus = "genus",
col_species = "species"))
expect_error(first_isolate(septic_patients %>%
mutate(mo = as.character(mo)) %>%
left_join_microorganisms()))
# if mo is not an mo class, result should be the same
expect_identical(septic_patients %>%
mutate(mo = as.character(mo)) %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"),
mutate(mo = as.character(mo)) %>%
first_isolate(col_date = "date",
col_mo = "mo",
col_patient_id = "patient_id"),
septic_patients %>%
first_isolate(col_date = "date",
col_mo = "mo",