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v0.7.0

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dr. M.S. (Matthijs) Berends
2019-06-03 17:45:22 +02:00
parent 702da574c0
commit 270aa0dd33
87 changed files with 507 additions and 544 deletions
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49
tests/testthat/test-mdro.R
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@ -24,17 +24,17 @@ 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(suppressWarnings(mdro(septic_patients, country = c("de", "nl"), info = TRUE)))
expect_error(suppressWarnings(mdro(septic_patients, col_mo = "invalid", info = TRUE)))
expect_error(mdro(septic_patients, country = "invalid", col_mo = "mo", info = TRUE))
expect_error(mdro(septic_patients, country = "fr", info = TRUE))
expect_error(mdro(septic_patients, country = c("de", "nl"), info = TRUE))
expect_error(mdro(septic_patients, col_mo = "invalid", info = TRUE))
outcome <- suppressWarnings(mdro(septic_patients))
outcome <- suppressWarnings(eucast_exceptional_phenotypes(septic_patients, info = TRUE))
outcome <- mdro(septic_patients)
outcome <- 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 <- mdro(septic_patients, "nl", info = TRUE)
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
@ -42,19 +42,14 @@ test_that("mdro works", {
expect_equal(outcome %>% freq() %>% pull(count),
c(1969, 25, 6)) # 1969 neg, 25 unconfirmed, 6 pos
expect_equal(
suppressWarnings(
brmo(septic_patients, info = FALSE)),
suppressWarnings(
mdro(septic_patients, country = "nl", info = FALSE)
)
)
expect_equal(brmo(septic_patients, info = FALSE),
mdro(septic_patients, country = "nl", info = FALSE))
# still working on German guidelines
expect_error(suppressWarnings(mrgn(septic_patients, info = TRUE)))
# test Dutch P. aeruginosa MDRO
expect_equal(suppressWarnings(
expect_equal(
as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
cfta = "S",
cipr = "S",
@ -65,9 +60,9 @@ test_that("mdro works", {
pita = "S"),
country = "nl",
col_mo = "mo",
info = FALSE))
), "Negative")
expect_equal(suppressWarnings(
info = FALSE)),
"Negative")
expect_equal(
as.character(mdro(data.frame(mo = as.mo("P. aeruginosa"),
cefta = "R",
cipr = "R",
@ -78,16 +73,14 @@ test_that("mdro works", {
pita = "R"),
country = "nl",
col_mo = "mo",
info = FALSE))
), "Positive")
info = FALSE)),
"Positive")
# MDR TB
expect_equal(
suppressWarnings(
# 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]
),
# 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))
sample_rsi <- function() {
@ -97,7 +90,7 @@ test_that("mdro works", {
replace = TRUE)
}
expect_gt(
suppressWarnings(
#suppressWarnings(
data.frame(rifampicin = sample_rsi(),
inh = sample_rsi(),
gatifloxacin = sample_rsi(),
@ -106,7 +99,9 @@ test_that("mdro works", {
MFX = sample_rsi(),
KAN = sample_rsi()) %>%
mdr_tb() %>%
n_distinct()),
n_distinct()
#)
,
2)
})