mirror of
https://github.com/msberends/AMR.git
synced 2024-12-26 08:46:11 +01:00
180 lines
7.2 KiB
R
Executable File
180 lines
7.2 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# Antimicrobial Resistance (AMR) Analysis #
|
|
# #
|
|
# SOURCE #
|
|
# https://gitlab.com/msberends/AMR #
|
|
# #
|
|
# LICENCE #
|
|
# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
|
|
# #
|
|
# This R package is free software; you can freely use and distribute #
|
|
# it for both personal and commercial purposes under the terms of the #
|
|
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
|
|
# the Free Software Foundation. #
|
|
# #
|
|
# This R package was created for academic research and was publicly #
|
|
# released in the hope that it will be useful, but it comes WITHOUT #
|
|
# ANY WARRANTY OR LIABILITY. #
|
|
# Visit our website for more info: https://msberends.gitlab.io/AMR. #
|
|
# ==================================================================== #
|
|
|
|
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$age, markdown = TRUE, title = "TITLE")))
|
|
|
|
# character
|
|
expect_output(suppressWarnings(print(freq(microorganisms$fullname))))
|
|
# mo
|
|
expect_output(print(freq(septic_patients$mo)))
|
|
# rsi
|
|
expect_output(print(freq(septic_patients$amox)))
|
|
# 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$age))))
|
|
# rsi
|
|
expect_output(print(freq(septic_patients$amcl)))
|
|
# hms
|
|
expect_output(suppressWarnings(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(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())
|
|
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(amox, quote = TRUE)))
|
|
expect_output(print(septic_patients %>% group_by(gender) %>% freq(amox, 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 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")
|
|
|
|
expect_error(septic_patients %>% freq(nonexisting))
|
|
expect_error(septic_patients %>% select(1:10) %>% freq())
|
|
expect_error(septic_patients %>% freq(peni, oxac, clox, amox, amcl,
|
|
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$amcl),
|
|
freq(septic_patients$amox))
|
|
))
|
|
expect_output(print(
|
|
diff(freq(septic_patients$age),
|
|
freq(septic_patients$age)) # "No differences found."
|
|
))
|
|
expect_error(print(
|
|
diff(freq(septic_patients$amcl),
|
|
"Just a string") # not a freq tbl
|
|
))
|
|
|
|
})
|
|
|