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Becker classification

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Lancefield classification
Added Lancefield groups to `microorganisms` data set
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-08-02 13:15:45 +02:00
parent edd2dd09dc
commit 6262315527
10 changed files with 161 additions and 26 deletions
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16
tests/testthat/test-first_isolate.R
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@ -1,7 +1,7 @@
context("first_isolate.R")
test_that("first isolates work", {
# septic_patients contains 1959 out of 2000 first isolates
# septic_patients contains 1331 out of 2000 first isolates
expect_equal(
sum(
first_isolate(tbl = septic_patients,
@ -10,9 +10,9 @@ test_that("first isolates work", {
col_bactid = "bactid",
info = TRUE),
na.rm = TRUE),
1326)
1331)
# septic_patients contains 1962 out of 2000 first *weighted* isolates
# septic_patients contains 1426 out of 2000 first *weighted* isolates
expect_equal(
suppressWarnings(
sum(
@ -24,8 +24,8 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1421)
# and 1961 when using points
1426)
# and 1430 when using points
expect_equal(
suppressWarnings(
sum(
@ -37,9 +37,9 @@ test_that("first isolates work", {
type = "points",
info = TRUE),
na.rm = TRUE)),
1425)
1430)
# septic_patients contains 1732 out of 2000 first non-ICU isolates
# septic_patients contains 1176 out of 2000 first non-ICU isolates
expect_equal(
sum(
first_isolate(septic_patients,
@ -50,7 +50,7 @@ test_that("first isolates work", {
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
1171)
1176)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)