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(v1.6.0.9050) printing NA in custom_eucast_rules()

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-05-20 10:10:40 +02:00
parent 9a2879cba9
commit 04ef5b28e7
21 changed files with 71 additions and 64 deletions
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5
inst/tinytest/test-atc_online.R
View File

@ -23,7 +23,10 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
if (tryCatch(curl::has_internet(), error = function(e) FALSE)) {
if (pkg_is_available("curl", also_load = FALSE) &&
pkg_is_available("rvest", also_load = FALSE) &&
pkg_is_available("xml2", also_load = FALSE) &&
tryCatch(curl::has_internet(), error = function(e) FALSE)) {
expect_true(length(atc_online_groups(ab_atc("AMX"))) >= 1)
expect_equal(atc_online_ddd(ab_atc("AMX"), administration = "O"), 1.5)
expect_equal(atc_online_ddd(ab_atc("AMX"), administration = "P"), 3)

20
inst/tinytest/test-proportion.R
View File

@ -35,17 +35,17 @@ expect_equal(proportion_R(example_isolates$AMX) + proportion_I(example_isolates$
expect_equal(proportion_S(example_isolates$AMX) + proportion_I(example_isolates$AMX),
proportion_SI(example_isolates$AMX))
expect_equal(example_isolates %>% proportion_SI(AMC),
0.7626397,
tolerance = 0.0001)
expect_equal(example_isolates %>% proportion_SI(AMC, GEN),
0.9408,
tolerance = 0.0001)
expect_equal(example_isolates %>% proportion_SI(AMC, GEN, only_all_tested = TRUE),
0.9382647,
tolerance = 0.0001)
if (pkg_is_available("dplyr")) {
expect_equal(example_isolates %>% proportion_SI(AMC),
0.7626397,
tolerance = 0.0001)
expect_equal(example_isolates %>% proportion_SI(AMC, GEN),
0.9408,
tolerance = 0.0001)
expect_equal(example_isolates %>% proportion_SI(AMC, GEN, only_all_tested = TRUE),
0.9382647,
tolerance = 0.0001)
# percentages
expect_equal(example_isolates %>%
group_by(hospital_id) %>%