P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 23:21:56 +02:00
Code Releases Activity

eucast update

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-11-01 20:23:33 +01:00
parent f7687557c9
commit 5476fecc73
16 changed files with 82 additions and 69 deletions
Download Patch File Download Diff File Expand all files Collapse all files

15
tests/testthat/test-eucast.R
View File

@ -2,8 +2,7 @@ context("eucast.R")
test_that("EUCAST rules work", {
expect_error(EUCAST_rules(septic_patients, col_mo = "Non-existing"))
expect_error(suppressWarnings(EUCAST_rules(septic_patients, col_mo = "Non-existing")))
expect_identical(colnames(septic_patients),
colnames(suppressWarnings(EUCAST_rules(septic_patients))))
@ -18,8 +17,8 @@ test_that("EUCAST rules work", {
"ENTAER"), # Enterobacter aerogenes
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
expect_identical(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
expect_identical(suppressWarnings(interpretive_reading(a, info = TRUE)), b)
expect_identical(suppressWarnings(EUCAST_rules(a, "mo", info = FALSE)), b)
expect_identical(suppressWarnings(interpretive_reading(a, "mo", info = TRUE)), b)
a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
@ -29,18 +28,18 @@ test_that("EUCAST rules work", {
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
coli = "R", # Colistin
stringsAsFactors = FALSE)
expect_equal(suppressWarnings(EUCAST_rules(a, info = FALSE)), b)
expect_equal(suppressWarnings(EUCAST_rules(a, "mo", info = FALSE)), b)
# pita must be R in Enterobacteriaceae when tica is R
# piperacillin must be R in Enterobacteriaceae when tica is R
library(dplyr)
expect_equal(suppressWarnings(
septic_patients %>%
mutate(tica = as.rsi("R"),
pita = as.rsi("S")) %>%
pipe = as.rsi("S")) %>%
EUCAST_rules(col_mo = "mo") %>%
left_join_microorganisms() %>%
filter(family == "Enterobacteriaceae") %>%
pull(pita) %>%
pull(pipe) %>%
unique() %>%
as.character()),
"R")