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count_all and some fixes

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-10-12 16:35:18 +02:00
parent e7d937d36e
commit 5b5b95a47b
22 changed files with 232 additions and 246 deletions
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4
tests/testthat/test-atc.R
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@ -10,8 +10,8 @@ test_that("atc_property works", {
expect_equal(atc_property("J01CA04", property = "DDD"),
atc_ddd("J01CA04"))
expect_identical(atc_property("J01CA04", property = "Groups"),
atc_groups("J01CA04"))
# expect_identical(atc_property("J01CA04", property = "Groups"),
# atc_groups("J01CA04"))
expect_warning(atc_property("ABCDEFG", property = "DDD"))

5
tests/testthat/test-count.R
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@ -10,8 +10,13 @@ test_that("counts work", {
expect_equal(count_S(septic_patients$amox) + count_I(septic_patients$amox),
count_SI(septic_patients$amox))
library(dplyr)
expect_equal(septic_patients %>% count_S(amcl), 1057)
expect_equal(septic_patients %>% count_S(amcl, gent), 1396)
expect_equal(septic_patients %>% count_all(amcl, gent), 1517)
expect_identical(septic_patients %>% count_all(amcl, gent),
septic_patients %>% count_S(amcl, gent) +
septic_patients %>% count_IR(amcl, gent))
# count of cases
expect_equal(septic_patients %>%

7
tests/testthat/test-freq.R
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@ -43,6 +43,11 @@ test_that("frequency table works", {
# list
expect_output(print(freq(list(age = septic_patients$age))))
expect_output(print(freq(list(age = septic_patients$age, gender = septic_patients$gender))))
# difftime
expect_output(suppressWarnings(print(
freq(difftime(Sys.time(),
Sys.time() - runif(5, min = 0, max = 60 * 60 * 24),
units = "hours")))))
library(dplyr)
expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())
@ -119,7 +124,7 @@ test_that("frequency table works", {
))
expect_output(print(
diff(freq(septic_patients$age),
freq(septic_patients$age)) # same
freq(septic_patients$age)) # "No differences found."
))
expect_error(print(
diff(freq(septic_patients$amcl),

6
tests/testthat/test-portion.R
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@ -68,11 +68,11 @@ test_that("portions works", {
expect_error(portion_S("test", as_percent = "test"))
# check too low amount of isolates
expect_identical(portion_R(septic_patients$amox, minimum = nrow(septic_patients) + 1),
expect_identical(suppressWarnings(portion_R(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
NA)
expect_identical(portion_I(septic_patients$amox, minimum = nrow(septic_patients) + 1),
expect_identical(suppressWarnings(portion_I(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
NA)
expect_identical(portion_S(septic_patients$amox, minimum = nrow(septic_patients) + 1),
expect_identical(suppressWarnings(portion_S(septic_patients$amox, minimum = nrow(septic_patients) + 1)),
NA)
# warning for speed loss