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(v1.4.0.9046) get_episode

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-12-27 00:07:00 +01:00
parent 291f802be3
commit acbd0cf7ca
99 changed files with 1143 additions and 683 deletions
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2
tests/testthat/test-count.R
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@ -79,7 +79,9 @@ test_that("counts work", {
)
# warning for speed loss
reset_all_thrown_messages()
expect_warning(count_resistant(as.character(example_isolates$AMC)))
reset_all_thrown_messages()
expect_warning(count_resistant(example_isolates$AMC,
as.character(example_isolates$GEN)))

2
tests/testthat/test-is_new_episode.R → tests/testthat/test-episode.R
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@ -23,7 +23,7 @@
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
context("is_new_episode.R")
context("episode.R")
test_that("new episodes work", {
skip_on_cran()

1
tests/testthat/test-filter_ab_class.R
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@ -28,6 +28,7 @@ context("filter_ab_class.R")
test_that("ATC-group filtering works", {
skip_on_cran()
library(dplyr)
expect_gt(example_isolates %>% filter_ab_class("carbapenem") %>% nrow(), 0)
expect_gt(example_isolates %>% filter_aminoglycosides() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_carbapenems() %>% nrow(), 0)

9
tests/testthat/test-proportion.R
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@ -76,11 +76,15 @@ test_that("proportions works", {
combination_n = n_rsi(CIP, GEN)) %>%
pull(combination_n),
c(305, 617, 241, 711))
reset_all_thrown_messages()
expect_warning(proportion_R(as.character(example_isolates$AMC)))
reset_all_thrown_messages()
expect_warning(proportion_S(as.character(example_isolates$AMC)))
reset_all_thrown_messages()
expect_warning(proportion_S(as.character(example_isolates$AMC,
example_isolates$GEN)))
reset_all_thrown_messages()
expect_warning(n_rsi(as.character(example_isolates$AMC,
example_isolates$GEN)))
expect_equal(suppressWarnings(n_rsi(as.character(example_isolates$AMC,
@ -105,8 +109,11 @@ test_that("proportions works", {
NA_real_)
# warning for speed loss
reset_all_thrown_messages()
expect_warning(proportion_R(as.character(example_isolates$GEN)))
reset_all_thrown_messages()
expect_warning(proportion_I(as.character(example_isolates$GEN)))
reset_all_thrown_messages()
expect_warning(proportion_S(example_isolates$AMC, as.character(example_isolates$GEN)))
# proportion_df