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extra unit tests

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dr. M.S. (Matthijs) Berends 2018-07-02 09:34:20 +02:00
parent 2c8d4cb8bf
commit a1acb2f3ac
4 changed files with 53 additions and 5 deletions
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33
tests/testthat/test-first_isolates.R
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@ -16,7 +16,8 @@ test_that("first isolates work", {
col_patient_id = "patient_id",
col_bactid = "bactid",
info = FALSE),
na.rm = TRUE), 1959)
na.rm = TRUE),
1959)
# septic_patients contains 1961 out of 2000 first *weighted* isolates
expect_equal(
@ -31,6 +32,19 @@ test_that("first isolates work", {
info = TRUE),
na.rm = TRUE)),
1961)
# and 1998 when using points
expect_equal(
suppressWarnings(
sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_keyantibiotics = "keyab",
type = "points",
info = TRUE),
na.rm = TRUE)),
1998)
# septic_patients contains 1732 out of 2000 first non-ICU isolates
expect_equal(
@ -61,4 +75,21 @@ test_that("first isolates work", {
info = TRUE),
na.rm = TRUE),
1501)
# same, but now exclude ICU
expect_lt(
sum(
first_isolate(tbl = mutate(septic_patients,
specimen = if_else(row_number() %in% random_rows,
"Urine",
"Unknown")),
col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid",
col_specimen = "specimen",
filter_specimen = "Urine",
col_icu = "ward_icu",
icu_exclude = TRUE,
info = TRUE),
na.rm = TRUE),
1501)
})

8
tests/testthat/test-freq.R
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@ -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), 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)
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)
# date column of septic_patients should contain 1662 unique dates
expect_equal(nrow(freq(septic_patients$date, as.data.frame = TRUE)), 1662)
expect_equal(nrow(freq(septic_patients$date, as.data.frame = TRUE)),
expect_equal(nrow(freq(septic_patients$date)), 1662)
expect_equal(nrow(freq(septic_patients$date)),
length(unique(septic_patients$date)))
# int

11
tests/testthat/test-g.test.R
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@ -2,6 +2,8 @@ context("g.test.R")
test_that("G-test works", {
# GOODNESS-OF-FIT
# example 1: clearfield rice vs. red rice
x <- c(772, 1611, 737)
x.expected <- vector2ratio(x, ratio = "1:2:1")
@ -16,4 +18,13 @@ test_that("G-test works", {
expected = 0.01787343,
tolerance = 0.00000001)
# INDEPENDENCE
# this should always yield a p value of around 0
x <- matrix(data = round(runif(4) * 100000, 0),
ncol = 2,
byrow = TRUE)
expect_lt(g.test(x),
0.0001)
})

6
tests/testthat/test-p.symbol.R Normal file
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@ -0,0 +1,6 @@
context("p.symbol.R")
test_that("P symbol works", {
expect_identical(p.symbol(c(0.001, 0.01, 0.05, 0.1, 1)),
c("***", "**", "*", ".", " "))
})