AMR/tests/testthat/test-freq.R

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R
Executable File

context("freq.R")
test_that("frequency table works", {
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 1151 unique dates
expect_equal(nrow(freq(septic_patients$date)), 1151)
expect_equal(nrow(freq(septic_patients$date)),
length(unique(septic_patients$date)))
# character
expect_output(print(freq(septic_patients$bactid)))
# integer
expect_output(print(freq(septic_patients$age)))
# date
expect_output(print(freq(septic_patients$date)))
# factor
expect_output(print(freq(septic_patients$hospital_id)))
# table
expect_output(print(freq(table(septic_patients$sex, septic_patients$age))))
# rsi
expect_output(print(freq(septic_patients$amcl)))
library(dplyr)
expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())
expect_output(septic_patients %>% select(1:3) %>% freq() %>% print())
expect_output(septic_patients %>% select(1:4) %>% freq() %>% print())
expect_output(septic_patients %>% select(1:5) %>% freq() %>% print())
expect_output(septic_patients %>% select(1:6) %>% freq() %>% print())
expect_output(septic_patients %>% select(1:7) %>% freq() %>% print())
expect_output(septic_patients %>% select(1:8) %>% freq() %>% print())
expect_output(septic_patients %>% select(1:9) %>% freq() %>% print())
# top 5
expect_equal(
septic_patients %>%
freq(bactid) %>%
top_freq(5) %>%
length(),
5)
# there're more than 5 lowest values
expect_gt(
septic_patients %>%
freq(bactid) %>%
top_freq(-5) %>%
length(),
5)
# n has length > 1
expect_error(
septic_patients %>%
freq(bactid) %>%
top_freq(n = c(1, 2))
)
# input must be freq tbl
expect_error(septic_patients %>% top_freq(1))
# charts from plot and hist, should not raise errors
plot(freq(septic_patients, age))
hist(freq(septic_patients, age))
# check vector
expect_identical(septic_patients %>%
freq(age) %>%
as.vector() %>%
sort(),
septic_patients %>%
pull(age) %>%
sort())
# check format
expect_identical(septic_patients %>%
freq(age) %>%
format() %>%
apply(2, class) %>%
unname(),
rep("character", 5))
# check tibble
expect_identical(septic_patients %>%
freq(age) %>%
as_tibble() %>%
class() %>%
.[1],
"tbl_df")
})