P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 09:11:51 +02:00
Code Releases Activity

removed ratio, better rsi_calc, update for freq

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-08-24 11:08:20 +02:00
parent 0c0e538ef4
commit a100d07da6
13 changed files with 116 additions and 140 deletions
Download Patch File Download Diff File Expand all files Collapse all files

6
tests/testthat/test-classes.R
View File

@ -28,9 +28,15 @@ test_that("mic works", {
expect_true(is.mic(as.mic(8)))
expect_equal(as.double(as.mic(">=32")), 32)
expect_equal(as.numeric(as.mic(">=32")), 32)
expect_equal(as.integer(as.mic(">=32")), 32)
expect_equal(suppressWarnings(as.logical(as.mic("INVALID VALUE"))), NA)
# all levels should be valid MICs
expect_silent(as.mic(levels(as.mic(1))))
expect_warning(as.mic("INVALID VALUE"))
# print plots, should not raise errors
barplot(as.mic(c(1, 2, 4, 8)))
plot(as.mic(c(1, 2, 4, 8)))

17
tests/testthat/test-freq.R
View File

@ -1,6 +1,8 @@
context("freq.R")
test_that("frequency table works", {
library(dplyr)
expect_equal(nrow(freq(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5))), 5)
expect_equal(nrow(frequency_tbl(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5))), 5)
@ -9,6 +11,7 @@ test_that("frequency table works", {
expect_equal(nrow(freq(septic_patients$date)),
length(unique(septic_patients$date)))
expect_output(print(septic_patients %>% freq(age, nmax = Inf)))
expect_output(print(freq(septic_patients$age, nmax = Inf)))
expect_output(print(freq(septic_patients$age, nmax = NA)))
expect_output(print(freq(septic_patients$age, nmax = NULL)))
@ -31,7 +34,13 @@ test_that("frequency table works", {
# rsi
expect_output(print(freq(septic_patients$amcl)))
# hms
expect_output(print(freq(hms::as.hms(sample(c(0:86399), 50)))))
expect_output(suppressWarnings(print(freq(hms::as.hms(sample(c(0:86399), 50))))))
# matrix
expect_output(print(freq(as.matrix(septic_patients$age))))
expect_output(print(freq(as.matrix(septic_patients[, c("age", "sex")]))))
# list
expect_output(print(freq(list(age = septic_patients$age))))
expect_output(print(freq(list(age = septic_patients$age, sex = septic_patients$sex))))
library(dplyr)
expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())
@ -94,5 +103,11 @@ test_that("frequency table works", {
class() %>%
.[1],
"tbl_df")
expect_error(septic_patients %>% freq(nonexisting))
expect_error(septic_patients %>% select(1:10) %>% freq())
expect_error(septic_patients %>% freq(peni, oxac, clox, amox, amcl,
ampi, pita, czol, cfep, cfur))
})

19
tests/testthat/test-g.test.R
View File

@ -6,24 +6,30 @@ test_that("G-test works", {
# example 1: clearfield rice vs. red rice
x <- c(772, 1611, 737)
x.expected <- ratio(x, ratio = "1:2:1")
expect_equal(g.test(x, p = c(0.25, 0.50, 0.25))$p.value,
expected = 0.12574,
tolerance = 0.00001)
# example 2: red crossbills
x <- c(1752, 1895)
x.expected <- ratio(x, c(1, 1))
expect_equal(g.test(x)$p.value,
expected = 0.01787343,
tolerance = 0.00000001)
expect_error(g.test(0))
expect_error(g.test(c(0, 1), 0))
expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25)))
expect_error(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24)))
expect_warning(g.test(c(1, 2, 3, 4), p = c(0.25, 0.25, 0.25, 0.24), rescale.p = TRUE))
# INDEPENDENCE
x <- matrix(data = round(runif(4) * 100000, 0),
ncol = 2,
byrow = TRUE)
x <- as.data.frame(
matrix(data = round(runif(4) * 100000, 0),
ncol = 2,
byrow = TRUE)
)
expect_lt(g.test(x)$p.value,
1)
@ -31,4 +37,7 @@ test_that("G-test works", {
y = c(780, 1560, 780),
rescale.p = TRUE))
expect_error(g.test(matrix(data = c(-1, -2, -3 , -4), ncol = 2, byrow = TRUE)))
expect_error(g.test(matrix(data = c(0, 0, 0, 0), ncol = 2, byrow = TRUE)))
})

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

@ -4,11 +4,12 @@ context("mdro.R")
test_that("MDRO works", {
library(dplyr)
outcome <- MDRO(septic_patients, "EUCAST", info = FALSE)
outcome <- suppressWarnings(MDRO(septic_patients, "EUCAST", info = TRUE))
outcome <- suppressWarnings(EUCAST_exceptional_phenotypes(septic_patients, info = TRUE))
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
outcome <- MDRO(septic_patients, "nl", info = FALSE)
outcome <- suppressWarnings(MDRO(septic_patients, "nl", info = TRUE))
# check class
expect_equal(outcome %>% class(), c('ordered', 'factor'))
@ -18,4 +19,7 @@ test_that("MDRO works", {
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)))
})