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(v1.5.0.9017) unit testing

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-02-08 21:09:36 +01:00
parent 4a84894f79
commit cb404492b2
20 changed files with 47 additions and 36 deletions
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1
tests/testthat/test-antibiotic_class_selectors.R → tests/testthat/test-ab_class_selectors.R
View File

@ -39,6 +39,7 @@ test_that("Antibiotic class selectors work", {
expect_lt(example_isolates %>% dplyr::select(fluoroquinolones()) %>% ncol(), ncol(example_isolates))
expect_lt(example_isolates %>% dplyr::select(glycopeptides()) %>% ncol(), ncol(example_isolates))
expect_lt(example_isolates %>% dplyr::select(macrolides()) %>% ncol(), ncol(example_isolates))
expect_lt(example_isolates %>% dplyr::select(oxazolidinones()) %>% ncol(), ncol(example_isolates))
expect_lt(example_isolates %>% dplyr::select(penicillins()) %>% ncol(), ncol(example_isolates))
expect_lt(example_isolates %>% dplyr::select(tetracyclines()) %>% ncol(), ncol(example_isolates))

25
tests/testthat/test-filter_ab_class.R
View File

@ -30,17 +30,20 @@ test_that("ATC-group filtering works", {
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)
expect_gt(example_isolates %>% filter_cephalosporins() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_1st_cephalosporins() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_2nd_cephalosporins() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_3rd_cephalosporins() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_4th_cephalosporins() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_fluoroquinolones() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_glycopeptides() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_macrolides() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_tetracyclines() %>% nrow(), 0)
expect_gt(example_isolates %>% filter_aminoglycosides() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_carbapenems() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_cephalosporins() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_1st_cephalosporins() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_2nd_cephalosporins() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_3rd_cephalosporins() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_4th_cephalosporins() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_5th_cephalosporins() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_fluoroquinolones() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_glycopeptides() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_macrolides() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_oxazolidinones() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_penicillins() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_tetracyclines() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_carbapenems("R", "all") %>% nrow(), 0)

6
tests/testthat/test-first_isolate.R
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@ -50,7 +50,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1396)
1395)
# when not ignoring I
expect_equal(
@ -65,7 +65,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1419)
1418)
# when using points
expect_equal(
suppressWarnings(
@ -78,7 +78,7 @@ test_that("first isolates work", {
type = "points",
info = TRUE),
na.rm = TRUE)),
1399)
1398)
# first non-ICU isolates
expect_equal(

7
tests/testthat/test-mdro.R
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@ -47,7 +47,7 @@ test_that("mdro works", {
library(dplyr)
# example_isolates should have these finding using Dutch guidelines
expect_equal(as.double(table(outcome)),
c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
c(1970, 24, 6)) # 1970 neg, 24 unconfirmed, 6 pos
expect_equal(brmo(example_isolates, info = FALSE),
mdro(example_isolates, guideline = "BRMO", info = FALSE))
@ -241,4 +241,9 @@ test_that("mdro works", {
guideline = custom_mdro_guideline(test ~ "A"),
info = FALSE))
# print groups
library(dplyr)
expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE))
expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE))
})