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mirror of https://github.com/msberends/AMR.git synced 2025-07-11 15:41:57 +02:00

new antibiotics

This commit is contained in:
2019-05-10 16:44:59 +02:00
parent 73f1ee1159
commit 68cc7ef0d0
147 changed files with 6228 additions and 4187 deletions

View File

@ -52,11 +52,11 @@ test_that("EUCAST rules work", {
a <- data.frame(mo = c("Staphylococcus aureus",
"Streptococcus group A"),
coli = "-", # Colistin
COL = "-", # Colistin
stringsAsFactors = FALSE)
b <- data.frame(mo = c("Staphylococcus aureus",
"Streptococcus group A"),
coli = "R", # Colistin
COL = "R", # Colistin
stringsAsFactors = FALSE)
expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
@ -64,30 +64,30 @@ test_that("EUCAST rules work", {
library(dplyr)
expect_equal(suppressWarnings(
septic_patients %>%
mutate(tica = as.rsi("R"),
pipe = as.rsi("S")) %>%
mutate(TIC = as.rsi("R"),
PIP = as.rsi("S")) %>%
eucast_rules(col_mo = "mo") %>%
left_join_microorganisms() %>%
filter(family == "Enterobacteriaceae") %>%
pull(pipe) %>%
pull(PIP) %>%
unique() %>%
as.character()),
"R")
# azit and clar must be equal to eryt
# Azithromicin and Clarythromycin must be equal to Erythromycin
a <- suppressWarnings(
septic_patients %>%
transmute(mo,
eryt,
azit = as.rsi("R"),
clar = as.rsi("R")) %>%
ERY,
AZM = as.rsi("R"),
CLR = as.rsi("R")) %>%
eucast_rules(col_mo = "mo") %>%
pull(clar))
pull(CLR))
b <- suppressWarnings(
septic_patients %>%
select(mo, eryt) %>%
select(mo, ERY) %>%
eucast_rules(col_mo = "mo") %>%
pull(eryt))
pull(ERY))
expect_identical(a[!is.na(b)],
b[!is.na(b)])
@ -97,15 +97,15 @@ test_that("EUCAST rules work", {
suppressWarnings(
as.list(eucast_rules(
data.frame(mo = as.mo("Kingella kingae"),
peni = "S",
amox = "-",
PEN = "S",
AMX = "-",
stringsAsFactors = FALSE)
, info = FALSE))$amox
, info = FALSE))$AMX
),
"S")
# also test norf
expect_output(suppressWarnings(eucast_rules(septic_patients %>% mutate(norf = "S", nali = "S"))))
expect_output(suppressWarnings(eucast_rules(septic_patients %>% mutate(NOR = "S", NAL = "S"))))
# check verbose output
expect_output(suppressWarnings(eucast_rules(septic_patients, verbose = TRUE)))