mirror of https://github.com/msberends/AMR.git
185 lines
7.4 KiB
R
Executable File
185 lines
7.4 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# SOURCE #
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# https://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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context("freq.R")
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test_that("frequency table works", {
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library(dplyr)
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expect_equal(nrow(freq(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5))), 5)
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expect_equal(nrow(frequency_tbl(c(1, 1, 2, 2, 3, 3, 4, 4, 5, 5))), 5)
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# date column of septic_patients should contain 1140 unique dates
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expect_equal(nrow(freq(septic_patients$date)), 1140)
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expect_equal(nrow(freq(septic_patients$date)),
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length(unique(septic_patients$date)))
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expect_output(print(septic_patients %>% freq(age)))
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expect_output(print(septic_patients %>% freq(age, nmax = 5)))
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expect_output(print(septic_patients %>% freq(age, nmax = Inf, markdown = FALSE)))
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expect_output(print(freq(septic_patients$age, nmax = Inf)))
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expect_output(print(freq(septic_patients$age, nmax = NA)))
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expect_output(print(freq(septic_patients$age, nmax = NULL)))
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expect_output(print(freq(septic_patients$age, sort.count = FALSE)))
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expect_output(print(freq(septic_patients$age, markdown = TRUE)))
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expect_output(print(freq(septic_patients$age, markdown = TRUE), markdown = FALSE))
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expect_output(print(freq(septic_patients$age, markdown = TRUE), markdown = TRUE))
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expect_output(print(freq(septic_patients$age[0])))
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expect_output(print(freq(septic_patients$age, quote = TRUE)))
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expect_output(print(freq(septic_patients$age, markdown = TRUE, title = "TITLE")))
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# character
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expect_output(print(freq(microorganisms$genus)))
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expect_output(print(structure(freq(microorganisms$genus),
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# check printing of old class:
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class = c("frequency_tbl", "data.frame"))))
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# mo
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expect_output(print(freq(septic_patients$mo)))
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# rsi
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expect_output(print(freq(septic_patients$AMX)))
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# integer
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expect_output(print(freq(septic_patients$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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expect_output(print(freq(table(septic_patients$gender, septic_patients$age))))
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# rsi
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expect_output(print(freq(septic_patients$AMC)))
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# hms
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expect_output(suppressWarnings(print(freq(hms::as.hms(sample(c(0:86399), 50))))))
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# matrix
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expect_output(print(freq(as.matrix(septic_patients$age))))
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expect_output(print(freq(as.matrix(septic_patients[, c("age", "gender")]))))
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# list
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expect_output(print(freq(list(age = septic_patients$age))))
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expect_output(print(freq(list(age = septic_patients$age, gender = septic_patients$gender))))
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# difftime
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expect_output(suppressWarnings(print(
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freq(difftime(Sys.time(),
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Sys.time() - runif(5, min = 0, max = 60 * 60 * 24),
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units = "hours")))))
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library(dplyr)
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expect_output(septic_patients %>% select(1:2) %>% freq() %>% print())
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expect_output(septic_patients %>% select(1:3) %>% freq() %>% print())
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expect_output(septic_patients %>% select(1:4) %>% freq() %>% print())
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expect_output(septic_patients %>% select(1:5) %>% freq() %>% print())
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expect_output(septic_patients %>% select(1:6) %>% freq() %>% print())
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expect_output(septic_patients %>% select(1:7) %>% freq() %>% print())
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expect_output(septic_patients %>% select(1:8) %>% freq() %>% print())
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expect_output(septic_patients %>% select(1:9) %>% freq() %>% print())
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expect_output(print(freq(septic_patients$age), nmax = 20))
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# grouping variable
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expect_output(print(septic_patients %>% group_by(gender) %>% freq(hospital_id)))
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expect_output(print(septic_patients %>% group_by(gender) %>% freq(AMX, quote = TRUE)))
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expect_output(print(septic_patients %>% group_by(gender) %>% freq(AMX, markdown = TRUE)))
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# quasiquotation
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expect_output(print(septic_patients %>% freq(mo_genus(mo))))
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expect_output(print(septic_patients %>% freq(mo, mo_genus(mo))))
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expect_output(print(septic_patients %>% group_by(gender) %>% freq(mo_genus(mo))))
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expect_output(print(septic_patients %>% group_by(gender) %>% freq(mo, mo_genus(mo))))
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# top 5
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expect_equal(
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septic_patients %>%
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freq(mo) %>%
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top_freq(5) %>%
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length(),
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5)
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# there are more than 5 lowest values
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expect_gt(
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septic_patients %>%
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freq(mo) %>%
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top_freq(-5) %>%
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length(),
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5)
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# n has length > 1
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expect_error(
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septic_patients %>%
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freq(mo) %>%
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top_freq(n = c(1, 2))
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)
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# input must be freq tbl
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expect_error(septic_patients %>% top_freq(1))
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# charts from plot, hist and boxplot, should not raise errors
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plot(freq(septic_patients, age))
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hist(freq(septic_patients, age))
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boxplot(freq(septic_patients, age))
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boxplot(freq(dplyr::group_by(septic_patients, gender), age))
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# check vector
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expect_identical(septic_patients %>%
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freq(age) %>%
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as.vector() %>%
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sort(),
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septic_patients %>%
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pull(age) %>%
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sort())
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# check format
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expect_identical(septic_patients %>%
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freq(age) %>%
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format() %>%
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apply(2, class) %>%
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unname(),
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rep("character", 5))
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# check tibble
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expect_identical(septic_patients %>%
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freq(age) %>%
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as_tibble() %>%
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class() %>%
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.[1],
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"tbl_df")
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expect_error(septic_patients %>% freq(nonexisting))
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expect_error(septic_patients %>% select(1:10) %>% freq())
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expect_error(septic_patients %>% freq(peni, oxac, clox, AMX, AMC,
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ampi, pita, czol, cfep, cfur))
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# (un)select columns
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expect_equal(septic_patients %>% freq(hospital_id) %>% select(item) %>% ncol(),
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1)
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expect_equal(septic_patients %>% freq(hospital_id) %>% select(-item) %>% ncol(),
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4)
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# run diff
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expect_output(print(
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diff(freq(septic_patients$AMC),
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freq(septic_patients$AMX))
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))
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expect_output(print(
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diff(freq(septic_patients$age),
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freq(septic_patients$age)) # "No differences found."
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))
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expect_error(print(
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diff(freq(septic_patients$AMX),
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"Just a string") # not a freq tbl
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))
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})
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