AMR/tests/testthat/test-freq.R

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context("freq.R")
test_that("frequency table works", {
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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
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expect_equal(nrow(freq(septic_patients$date)), 1662)
expect_equal(nrow(freq(septic_patients$date)),
length(unique(septic_patients$date)))
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# character
expect_output(print(freq(septic_patients$bactid)))
# integer
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expect_output(print(freq(septic_patients$age)))
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# date
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expect_output(print(freq(septic_patients$date)))
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# factor
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expect_output(print(freq(septic_patients$hospital_id)))
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# table
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if (Sys.info()['sysname'] %in% c("Windows", "Linux")) {
expect_output(print(freq(table(septic_patients$sex, septic_patients$age))))
}
library(dplyr)
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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())
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# top 5
expect_equal(
septic_patients %>%
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freq(bactid) %>%
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top_freq(5) %>%
length(),
5)
# there're more than 5 lowest values
expect_gt(
septic_patients %>%
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freq(bactid) %>%
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top_freq(-5) %>%
length(),
5)
# n has length > 1
expect_error(
septic_patients %>%
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freq(bactid) %>%
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top_freq(n = c(1, 2))
)
# input must be freq tbl
expect_error(septic_patients %>% top_freq(1))
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# charts from plot and hist, should not raise errors
plot(freq(septic_patients, age))
hist(freq(septic_patients, age))
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# check vector
expect_identical(septic_patients %>%
freq(age) %>%
as.vector() %>%
sort(),
septic_patients %>%
pull(age) %>%
sort())
})