P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 06:51:48 +02:00
Code Releases Activity

added vignette of freq

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-05-09 11:44:46 +02:00
parent 25b3346d9a
commit f05e7178cb
13 changed files with 726 additions and 82 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
tests/testthat/test-eucast.R
View File

@ -1,7 +1,7 @@
context("eucast.R")
test_that("EUCAST rules work", {
a <- EUCAST_rules(septic_patients)
a <- suppressWarnings(EUCAST_rules(septic_patients))
a <- data.frame(bactid = c("KLEPNE", # Klebsiella pneumoniae
"PSEAER", # Pseudomonas aeruginosa

8
tests/testthat/test-freq.R
View File

@ -1,12 +1,12 @@
context("freq.R")
test_that("frequency table works", {
expect_equal(nrow(freq(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5), toConsole = FALSE)), 5)
expect_equal(nrow(frequency_tbl(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5), toConsole = FALSE)), 5)
expect_equal(nrow(freq(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5), as.data.frame = TRUE)), 5)
expect_equal(nrow(frequency_tbl(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5), as.data.frame = TRUE)), 5)
# date column of septic_patients should contain 1662 unique dates
expect_equal(nrow(freq(septic_patients$date, toConsole = FALSE)), 1662)
expect_equal(nrow(freq(septic_patients$date, toConsole = FALSE)),
expect_equal(nrow(freq(septic_patients$date, as.data.frame = TRUE)), 1662)
expect_equal(nrow(freq(septic_patients$date, as.data.frame = TRUE)),
length(unique(septic_patients$date)))
expect_output(freq(septic_patients$age))

2
tests/testthat/test-mdro.R
View File

@ -13,7 +13,7 @@ test_that("MDRO works", {
expect_equal(outcome %>% class(), c('ordered', 'factor'))
# septic_patients should have these finding using Dutch guidelines
expect_equal(outcome %>% freq(toConsole = FALSE) %>% pull(Count), c(3, 21))
expect_equal(outcome %>% freq(as.data.frame = TRUE) %>% pull(count), c(3, 21))
expect_equal(BRMO(septic_patients, info = FALSE), MDRO(septic_patients, "nl", info = FALSE))