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Catalogue of Life, replaces ITIS

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-02-18 02:33:37 +01:00
parent 9209787a53
commit 54f8258f8c
88 changed files with 607 additions and 590 deletions
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22
tests/testthat/test-first_isolate.R
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@ -22,7 +22,7 @@
context("first_isolate.R")
test_that("first isolates work", {
# septic_patients contains 1317 out of 2000 first isolates
# first isolates
expect_equal(
sum(
first_isolate(tbl = septic_patients,
@ -31,9 +31,9 @@ test_that("first isolates work", {
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1317)
1274)
# septic_patients contains 1413 out of 2000 first *weighted* isolates
# first *weighted* isolates
expect_equal(
suppressWarnings(
sum(
@ -46,7 +46,7 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1413)
1369)
# should be same for tibbles
expect_equal(
suppressWarnings(
@ -60,8 +60,8 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1413)
# and 1436 when not ignoring I
1369)
# when not ignoring I
expect_equal(
suppressWarnings(
sum(
@ -74,8 +74,8 @@ test_that("first isolates work", {
type = "keyantibiotics",
info = TRUE),
na.rm = TRUE)),
1436)
# and 1417 when using points
1392)
# when using points
expect_equal(
suppressWarnings(
sum(
@ -87,9 +87,9 @@ test_that("first isolates work", {
type = "points",
info = TRUE),
na.rm = TRUE)),
1417)
1372)
# septic_patients contains 1163 out of 2000 first non-ICU isolates
# first non-ICU isolates
expect_equal(
sum(
first_isolate(septic_patients,
@ -100,7 +100,7 @@ test_that("first isolates work", {
info = TRUE,
icu_exclude = TRUE),
na.rm = TRUE),
1163)
1129)
# set 1500 random observations to be of specimen type 'Urine'
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)