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(v0.7.1.9015) Remove freq()

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dr. M.S. (Matthijs) Berends
2019-07-29 13:33:48 +02:00
parent 9ac5a34b36
commit 240f03a672
75 changed files with 668 additions and 2877 deletions
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160
tests/testthat/test-freq.R
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@ -22,168 +22,10 @@
context("freq.R")
test_that("frequency table works", {
library(dplyr)
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 1140 unique dates
expect_equal(nrow(freq(septic_patients$date)), 1140)
expect_equal(nrow(freq(septic_patients$date)),
length(unique(septic_patients$date)))
expect_output(print(septic_patients %>% freq(age)))
expect_output(print(septic_patients %>% freq(age, nmax = 5)))
expect_output(print(septic_patients %>% freq(age, nmax = Inf, markdown = FALSE)))
expect_output(print(freq(septic_patients$age, nmax = Inf)))
expect_output(print(freq(septic_patients$age, nmax = NA)))
expect_output(print(freq(septic_patients$age, nmax = NULL)))
expect_output(print(freq(septic_patients$age, sort.count = FALSE)))
expect_output(print(freq(septic_patients$age, markdown = TRUE)))
expect_output(print(freq(septic_patients$age, markdown = TRUE), markdown = FALSE))
expect_output(print(freq(septic_patients$age, markdown = TRUE), markdown = TRUE))
expect_output(print(freq(septic_patients$age[0])))
expect_output(print(freq(septic_patients$age, quote = TRUE)))
expect_output(print(freq(septic_patients$age, markdown = TRUE, title = "TITLE")))
# character
expect_output(print(freq(microorganisms$genus)))
expect_output(print(structure(freq(microorganisms$genus),
# check printing of old class:
class = c("frequency_tbl", "data.frame"))))
library(clean)
# mo
expect_output(print(freq(septic_patients$mo)))
# rsi
expect_output(print(freq(septic_patients$AMX)))
# integer
expect_output(print(freq(septic_patients$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$gender, septic_patients$age))))
# rsi
expect_output(print(freq(septic_patients$AMC)))
# hms
expect_output(print(freq(hms::as.hms(sample(c(0:86399), 50)))))
# matrix
expect_output(print(freq(as.matrix(septic_patients$age))))
expect_output(print(freq(as.matrix(septic_patients[, c("age", "gender")]))))
# list
expect_output(print(freq(list(age = septic_patients$age))))
expect_output(print(freq(list(age = septic_patients$age, gender = septic_patients$gender))))
# difftime
expect_output(print(
freq(difftime(Sys.time(),
Sys.time() - runif(5, min = 0, max = 60 * 60 * 24),
units = "hours"))))
expect_output(print(freq(septic_patients$age)[,1:3]))
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())
expect_output(print(freq(septic_patients$age), nmax = 20))
# grouping variable
expect_output(print(septic_patients %>% group_by(gender) %>% freq(hospital_id)))
expect_output(print(septic_patients %>% group_by(gender) %>% freq(AMX, quote = TRUE)))
expect_output(print(septic_patients %>% group_by(gender) %>% freq(AMX, markdown = TRUE)))
# quasiquotation
expect_output(print(septic_patients %>% freq(mo_genus(mo))))
expect_output(print(septic_patients %>% freq(mo, mo_genus(mo))))
expect_output(print(septic_patients %>% group_by(gender) %>% freq(mo_genus(mo))))
expect_output(print(septic_patients %>% group_by(gender) %>% freq(mo, mo_genus(mo))))
# top 5
expect_equal(
septic_patients %>%
freq(mo) %>%
top_freq(5) %>%
length(),
5)
# there are more than 5 lowest values
expect_gt(
septic_patients %>%
freq(mo) %>%
top_freq(-5) %>%
length(),
5)
# n has length > 1
expect_error(
septic_patients %>%
freq(mo) %>%
top_freq(n = c(1, 2))
)
# input must be freq tbl
expect_error(septic_patients %>% top_freq(1))
# charts from plot, hist and boxplot, should not raise errors
plot(freq(septic_patients, age))
hist(freq(septic_patients, age))
boxplot(freq(septic_patients, age))
boxplot(freq(dplyr::group_by(septic_patients, gender), 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")
expect_error(septic_patients %>% freq(nonexisting))
expect_error(septic_patients %>% select(1:10) %>% freq())
expect_error(septic_patients %>% freq(peni, oxac, clox, AMX, AMC,
ampi, pita, czol, cfep, cfur))
# (un)select columns
expect_equal(septic_patients %>% freq(hospital_id) %>% select(item) %>% ncol(),
1)
expect_equal(septic_patients %>% freq(hospital_id) %>% select(-item) %>% ncol(),
4)
# run diff
expect_output(print(
diff(freq(septic_patients$AMC),
freq(septic_patients$AMX))
))
expect_output(print(
diff(freq(septic_patients$age),
freq(septic_patients$age)) # "No differences found."
))
expect_error(print(
diff(freq(septic_patients$AMX),
"Just a string") # not a freq tbl
))
# directly on group
expect_output(print(septic_patients %>% group_by(ageplusone = as.character(age + 1)) %>% freq(ageplusone)))
})