P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-09 00:02:38 +02:00
Code Releases Activity

Welcome C++!

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-07-13 17:23:46 +02:00
parent a28289562a
commit b6655f6454
19 changed files with 469 additions and 435 deletions
Download Patch File Download Diff File Expand all files Collapse all files

45
tests/testthat/test-rsi_analysis.R → tests/testthat/test-resistance.R
View File

@ -1,46 +1,29 @@
context("rsi_analysis.R")
context("resistance.R")
test_that("resistance works", {
# amox resistance in `septic_patients` should be around 57.56%
expect_equal(resistance(septic_patients$amox), 0.5756, tolerance = 0.0001)
expect_equal(susceptibility(septic_patients$amox), 1 - 0.5756, tolerance = 0.0001)
test_that("rsi works", {
# amox resistance in `septic_patients` should be around 53.86%
expect_equal(rsi(septic_patients$amox), 0.5756, tolerance = 0.0001)
expect_equal(rsi(septic_patients$amox), 0.5756, tolerance = 0.0001)
expect_equal(rsi_df(septic_patients,
ab = "amox",
info = FALSE),
0.5756,
tolerance = 0.0001)
# pita+genta susceptibility around 98.09%
expect_equal(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S",
info = TRUE),
expect_equal(susceptibility(septic_patients$pita,
septic_patients$gent),
0.9809,
tolerance = 0.0001)
expect_equal(rsi_df(septic_patients,
ab = c("pita", "gent"),
interpretation = "S",
info = FALSE),
expect_equal(suppressWarnings(rsi(septic_patients$pita,
septic_patients$gent,
interpretation = "S")),
0.9809,
tolerance = 0.0001)
# mero+pita+genta susceptibility around 98.58%
expect_equal(rsi_df(septic_patients,
ab = c("mero", "pita", "gent"),
interpretation = "IS",
info = FALSE),
0.9858,
tolerance = 0.0001)
# count of cases
expect_equal(septic_patients %>%
group_by(hospital_id) %>%
summarise(cipro_S = rsi(cipr, interpretation = "S",
as_percent = TRUE, warning = FALSE),
summarise(cipro_p = susceptibility(cipr, as_percent = TRUE),
cipro_n = n_rsi(cipr),
genta_S = rsi(gent, interpretation = "S",
as_percent = TRUE, warning = FALSE),
genta_p = susceptibility(gent, as_percent = TRUE),
genta_n = n_rsi(gent),
combination_S = rsi(cipr, gent, interpretation = "S",
as_percent = TRUE, warning = FALSE),
combination_p = susceptibility(cipr, gent, as_percent = TRUE),
combination_n = n_rsi(cipr, gent)) %>%
pull(combination_n),
c(138, 474, 170, 464, 183))