P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 15:21:58 +02:00
Code Releases Activity

first isolate missing dates fix

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-05-13 14:56:23 +02:00
parent c4aa92b4a7
commit cc403169c6
15 changed files with 200 additions and 146 deletions
Download Patch File Download Diff File Expand all files Collapse all files

26
tests/testthat/test-first_isolate.R
View File

@ -25,7 +25,7 @@ test_that("first isolates work", {
# first isolates
expect_equal(
sum(
first_isolate(tbl = septic_patients,
first_isolate(x = septic_patients,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
@ -37,7 +37,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = septic_patients %>% mutate(keyab = key_antibiotics(.)),
# let syntax determine these automatically:
# col_date = "date",
# col_patient_id = "patient_id",
@ -51,7 +51,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% dplyr::as_tibble() %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = septic_patients %>% dplyr::as_tibble() %>% mutate(keyab = key_antibiotics(.)),
# let syntax determine these automatically:
# col_date = "date",
# col_patient_id = "patient_id",
@ -65,7 +65,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
@ -79,7 +79,7 @@ test_that("first isolates work", {
expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
first_isolate(x = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
@ -106,7 +106,7 @@ test_that("first isolates work", {
random_rows <- sample(x = 1:2000, size = 1500, replace = FALSE)
expect_lt(
sum(
first_isolate(tbl = mutate(septic_patients,
first_isolate(x = mutate(septic_patients,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Other")),
@ -121,7 +121,7 @@ test_that("first isolates work", {
# same, but now exclude ICU
expect_lt(
sum(
first_isolate(tbl = mutate(septic_patients,
first_isolate(x = mutate(septic_patients,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Other")),
@ -175,4 +175,16 @@ test_that("first isolates work", {
col_mo = "mo",
col_patient_id = "patient_id"))
df <- septic_patients
df[1:100, "date"] <- NA
expect_equal(
sum(
first_isolate(x = df,
col_date = "date",
col_patient_id = "patient_id",
col_mo = "mo",
info = TRUE),
na.rm = TRUE),
1279)
})