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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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22
tests/testthat/test-mdro.R
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@ -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)))
})