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(v1.4.0.9043) documentation update

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-12-22 00:51:17 +01:00
parent ee70883246
commit 128ebcfd62
107 changed files with 518 additions and 475 deletions
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47
tests/testthat/test-rsi.R
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@ -26,6 +26,7 @@
context("rsi.R")
test_that("rsi works", {
skip_on_cran()
expect_true(as.rsi("S") < as.rsi("I"))
@ -83,7 +84,6 @@ test_that("rsi works", {
})
test_that("mic2rsi works", {
skip_on_cran()
@ -115,19 +115,6 @@ test_that("mic2rsi works", {
as.rsi() %>%
pull(amox_mic) %>%
is.rsi()))
expect_warning(data.frame(mo = "E. coli",
NIT = c("<= 2", 32)) %>%
as.rsi())
expect_message(data.frame(mo = "E. coli",
NIT = c("<= 2", 32),
uti = TRUE) %>%
as.rsi())
expect_message(
data.frame(mo = "E. coli",
NIT = c("<= 2", 32),
specimen = c("urine", "blood")) %>%
as.rsi())
})
test_that("disk2rsi works", {
@ -160,11 +147,37 @@ test_that("disk2rsi works", {
pull(amox_disk) %>%
is.rsi())
expect_s3_class(suppressWarnings(as.rsi(data.frame(mo = "Escherichia coli",
amoxi = c("R", "S", "I", "invalid")))$amoxi), "rsi")
# frequency tables
if (require("cleaner")) {
expect_s3_class(cleaner::freq(example_isolates$AMX), "freq")
}
})
test_that("data.frame2rsi works", {
skip_on_cran()
df <- data.frame(microorganism = "Escherichia coli",
AMP = as.mic(8),
CIP = as.mic(0.256),
GEN = as.disk(18),
TOB = as.disk(16),
ERY = "R", # note about assigning <rsi> class
CLR = "V") # note about cleaning
expect_s3_class(as.rsi(df), "data.frame")
expect_s3_class(suppressWarnings(as.rsi(data.frame(mo = "Escherichia coli",
amoxi = c("R", "S", "I", "invalid")))$amoxi), "rsi")
expect_warning(data.frame(mo = "E. coli",
NIT = c("<= 2", 32)) %>%
as.rsi())
expect_message(data.frame(mo = "E. coli",
NIT = c("<= 2", 32),
uti = TRUE) %>%
as.rsi())
expect_message(
data.frame(mo = "E. coli",
NIT = c("<= 2", 32),
specimen = c("urine", "blood")) %>%
as.rsi())
})