mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 08:32:04 +02:00
first isolate missing dates fix
This commit is contained in:
@ -42,9 +42,12 @@ test_that("as.ab works", {
|
||||
|
||||
expect_warning(as.ab("Z00ZZ00")) # not yet available in data set
|
||||
expect_warning(as.ab("UNKNOWN"))
|
||||
expect_warning(as.ab(""))
|
||||
|
||||
expect_output(print(as.ab("amox")))
|
||||
|
||||
expect_identical(class(pull(antibiotics, ab)), "ab")
|
||||
|
||||
# first 5 chars of official name
|
||||
expect_equal(as.character(as.atc(c("nitro", "cipro"))),
|
||||
c("J01XE01", "J01MA02"))
|
||||
@ -53,4 +56,7 @@ test_that("as.ab works", {
|
||||
expect_equal(as.character(as.atc("AMX")),
|
||||
"J01CA04")
|
||||
|
||||
expect_equal(as.character(as.ab("Phloxapen")),
|
||||
"FLC")
|
||||
|
||||
})
|
||||
|
||||
@ -48,4 +48,6 @@ test_that("creation of data sets is valid", {
|
||||
test_that("CoL version info works", {
|
||||
expect_identical(class(catalogue_of_life_version()),
|
||||
c("catalogue_of_life_version", "list"))
|
||||
|
||||
expect_output(print(catalogue_of_life_version()))
|
||||
})
|
||||
|
||||
35
tests/testthat/test-disk.R
Executable file
35
tests/testthat/test-disk.R
Executable file
@ -0,0 +1,35 @@
|
||||
# ==================================================================== #
|
||||
# TITLE #
|
||||
# Antidiskrobial Resistance (AMR) Analysis #
|
||||
# #
|
||||
# SOURCE #
|
||||
# https://gitlab.com/msberends/AMR #
|
||||
# #
|
||||
# LICENCE #
|
||||
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
||||
# #
|
||||
# This R package is free software; you can freely use and distribute #
|
||||
# it for both personal and commercial purposes under the terms of the #
|
||||
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
||||
# the Free Software Foundation. #
|
||||
# #
|
||||
# This R package was created for academic research and was publicly #
|
||||
# released in the hope that it will be useful, but it comes WITHOUT #
|
||||
# ANY WARRANTY OR LIABILITY. #
|
||||
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
||||
# ==================================================================== #
|
||||
|
||||
context("disk.R")
|
||||
|
||||
test_that("disk works", {
|
||||
expect_true(as.disk(8) == as.disk("8"))
|
||||
expect_true(is.disk(as.disk(8)))
|
||||
|
||||
expect_equal(suppressWarnings(as.logical(as.disk("INVALID VALUE"))), NA)
|
||||
|
||||
# all levels should be valid disks
|
||||
expect_silent(as.disk(levels(as.disk(15))))
|
||||
|
||||
expect_warning(as.disk("INVALID VALUE"))
|
||||
|
||||
})
|
||||
@ -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)
|
||||
|
||||
})
|
||||
|
||||
Reference in New Issue
Block a user