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(v0.7.1.9063) septic_patients -> example_isolates

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dr. M.S. (Matthijs) Berends
2019-08-27 16:45:42 +02:00
parent 7a6fce4eb8
commit 93be16484b
92 changed files with 1143 additions and 818 deletions
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26
tests/testthat/test-mdro.R
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@ -24,29 +24,29 @@ context("mdro.R")
test_that("mdro works", {
library(dplyr)
expect_error(suppressWarnings(mdro(septic_patients, country = "invalid", col_mo = "mo", info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, country = "fr", info = TRUE)))
expect_error(mdro(septic_patients, guideline = c("BRMO", "MRGN"), info = TRUE))
expect_error(mdro(septic_patients, col_mo = "invalid", info = TRUE))
expect_error(suppressWarnings(mdro(example_isolates, country = "invalid", col_mo = "mo", info = TRUE)))
expect_error(suppressWarnings(mdro(example_isolates, country = "fr", info = TRUE)))
expect_error(mdro(example_isolates, guideline = c("BRMO", "MRGN"), info = TRUE))
expect_error(mdro(example_isolates, col_mo = "invalid", info = TRUE))
outcome <- mdro(septic_patients)
outcome <- eucast_exceptional_phenotypes(septic_patients, info = TRUE)
outcome <- mdro(example_isolates)
outcome <- eucast_exceptional_phenotypes(example_isolates, info = TRUE)
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
outcome <- mdro(septic_patients, "nl", info = TRUE)
outcome <- mdro(example_isolates, "nl", info = TRUE)
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
# septic_patients should have these finding using Dutch guidelines
# example_isolates should have these finding using Dutch guidelines
expect_equal(outcome %>% freq() %>% pull(count),
c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
expect_equal(brmo(septic_patients, info = FALSE),
mdro(septic_patients, guideline = "BRMO", info = FALSE))
expect_equal(brmo(example_isolates, info = FALSE),
mdro(example_isolates, guideline = "BRMO", info = FALSE))
# still working on German guidelines
expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
expect_error(suppressWarnings(mrgn(example_isolates, info = TRUE)))
# test Dutch P. aeruginosa MDRO
expect_equal(
@ -80,8 +80,8 @@ test_that("mdro works", {
expect_equal(
# select only rifampicine, mo will be determined automatically (as M. tuberculosis),
# number of mono-resistant strains should be equal to number of rifampicine-resistant strains
septic_patients %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2],
count_R(septic_patients$RIF))
example_isolates %>% select(RIF) %>% mdr_tb() %>% freq() %>% pull(count) %>% .[2],
count_R(example_isolates$RIF))
sample_rsi <- function() {
sample(c("S", "I", "R"),