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MDRO update

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-11-16 20:50:50 +01:00
parent fab64e6728
commit 4fcc2b409a
10 changed files with 207 additions and 186 deletions
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21
tests/testthat/test-eucast.R → tests/testthat/test-eucast_rules.R
View File

@ -1,11 +1,11 @@
context("eucast.R")
context("eucast_rules.R")
test_that("EUCAST rules work", {
expect_error(suppressWarnings(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))))
colnames(suppressWarnings(eucast_rules(septic_patients))))
a <- data.frame(mo = c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa
@ -17,7 +17,8 @@ test_that("EUCAST rules work", {
"ENTAER"), # Enterobacter aerogenes
amox = "R", # Amoxicillin
stringsAsFactors = FALSE)
expect_identical(suppressWarnings(EUCAST_rules(a, "mo", info = FALSE)), b)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
expect_identical(suppressWarnings(eucast_rules(a, "mo", info = TRUE)), b)
expect_identical(suppressWarnings(interpretive_reading(a, "mo", info = TRUE)), b)
a <- data.frame(mo = c("STAAUR", # Staphylococcus aureus
@ -28,7 +29,7 @@ test_that("EUCAST rules work", {
"STCGRA"), # Streptococcus pyognenes (Lancefield Group A)
coli = "R", # Colistin
stringsAsFactors = FALSE)
expect_equal(suppressWarnings(EUCAST_rules(a, "mo", info = FALSE)), b)
expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
# piperacillin must be R in Enterobacteriaceae when tica is R
library(dplyr)
@ -36,7 +37,7 @@ test_that("EUCAST rules work", {
septic_patients %>%
mutate(tica = as.rsi("R"),
pipe = as.rsi("S")) %>%
EUCAST_rules(col_mo = "mo") %>%
eucast_rules(col_mo = "mo") %>%
left_join_microorganisms() %>%
filter(family == "Enterobacteriaceae") %>%
pull(pipe) %>%
@ -51,12 +52,12 @@ test_that("EUCAST rules work", {
eryt,
azit = as.rsi("R"),
clar = as.rsi("R")) %>%
EUCAST_rules(col_mo = "mo") %>%
eucast_rules(col_mo = "mo") %>%
pull(clar))
b <- suppressWarnings(
septic_patients %>%
select(mo, eryt) %>%
EUCAST_rules(col_mo = "mo") %>%
eucast_rules(col_mo = "mo") %>%
pull(eryt))
expect_identical(a[!is.na(b)],
@ -64,7 +65,7 @@ test_that("EUCAST rules work", {
# amox is inferred by benzylpenicillin in Kingella kingae
expect_equal(
as.list(EUCAST_rules(
as.list(eucast_rules(
data.frame(mo = as.mo("Kingella kingae"),
peni = "S",
amox = "-",
@ -72,6 +73,6 @@ test_that("EUCAST rules work", {
, info = FALSE))$amox,
"S")
expect_output(suppressWarnings(EUCAST_rules(septic_patients, verbose = TRUE)))
expect_output(suppressWarnings(eucast_rules(septic_patients, verbose = TRUE)))
})

22
tests/testthat/test-mdro.R
View File

@ -1,30 +1,30 @@
context("mdro.R")
test_that("MDRO works", {
test_that("mdro works", {
library(dplyr)
expect_error(suppressWarnings(MDRO(septic_patients, "invalid", col_bactid = "mo", info = TRUE)))
expect_error(suppressWarnings(MDRO(septic_patients, "fr", col_bactid = "mo", info = TRUE)))
expect_error(suppressWarnings(MDRO(septic_patients, country = c("de", "nl"), info = TRUE)))
expect_error(suppressWarnings(MDRO(septic_patients, col_mo = "invalid", info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, "invalid", col_bactid = "mo", info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, "fr", col_bactid = "mo", info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, country = c("de", "nl"), info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, col_mo = "invalid", info = TRUE)))
outcome <- suppressWarnings(MDRO(septic_patients))
outcome <- suppressWarnings(EUCAST_exceptional_phenotypes(septic_patients, info = TRUE))
outcome <- suppressWarnings(mdro(septic_patients))
outcome <- suppressWarnings(eucast_exceptional_phenotypes(septic_patients, info = TRUE))
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
outcome <- suppressWarnings(MDRO(septic_patients, "nl", info = TRUE))
outcome <- suppressWarnings(mdro(septic_patients, "nl", info = TRUE))
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
# septic_patients should have these finding using Dutch guidelines
expect_equal(outcome %>% freq() %>% pull(count),
c(1167, 817, 14, 2)) # 1167 not eval., 817 neg, 14 pos, 2 unconfirmed
c(19989, 9, 2)) # 1167 not eval., 817 neg, 14 pos, 2 unconfirmed
expect_equal(BRMO(septic_patients, info = FALSE), MDRO(septic_patients, "nl", info = FALSE))
expect_equal(brmo(septic_patients, info = FALSE), mdro(septic_patients, "nl", info = FALSE))
# still working on German guidelines
expect_error(suppressWarnings(MRGN(septic_patients, info = TRUE)))
expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
})