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mirror of https://github.com/msberends/AMR.git synced 2025-07-08 18:41:58 +02:00

(v1.3.0) skip more CRAN tests

This commit is contained in:
2020-07-31 10:50:08 +02:00
parent c8edcb7439
commit c5f7294381
45 changed files with 66 additions and 65 deletions

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@ -22,7 +22,6 @@
context("ab.R")
test_that("as.ab works", {
skip_on_cran()
expect_equal(as.character(as.ab(c("J01FA01",

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@ -22,7 +22,6 @@
context("ab_from_text.R")
test_that("ab_from_text works", {
skip_on_cran()
expect_identical(ab_from_text("28/03/2020 regular amoxicilliin 500mg po tds")[[1]],

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@ -22,7 +22,6 @@
context("ab_property.R")
test_that("ab_property works", {
skip_on_cran()
expect_identical(ab_name("AMX"), "Amoxicillin")

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@ -22,6 +22,7 @@
context("age.R")
test_that("age works", {
skip_on_cran()
expect_equal(age(x = c("1980-01-01", "1985-01-01", "1990-01-01"),
reference = "2019-01-01"),
c(39, 34, 29))
@ -47,6 +48,7 @@ test_that("age works", {
})
test_that("age_groups works", {
skip_on_cran()
ages <- c(3, 8, 16, 54, 31, 76, 101, 43, 21)
expect_equal(length(unique(age_groups(ages, 50))),

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@ -22,5 +22,6 @@
context("availability.R")
test_that("availability works", {
skip_on_cran()
expect_equal(class(availability(example_isolates)), "data.frame")
})

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@ -22,7 +22,6 @@
context("bug_drug_combinations.R")
test_that("bug_drug_combinations works", {
skip_on_cran()
b <- suppressWarnings(bug_drug_combinations(example_isolates))

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@ -22,7 +22,6 @@
context("count.R")
test_that("counts work", {
skip_on_cran()
expect_equal(count_resistant(example_isolates$AMX), count_R(example_isolates$AMX))

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@ -22,7 +22,7 @@
context("data.R")
test_that("data sets are valid", {
skip_on_cran()
expect_true(check_dataset_integrity()) # in misc.R
# IDs should always be unique
@ -39,10 +39,10 @@ test_that("data sets are valid", {
expect_false(any(is.na(microorganisms.codes$code)))
expect_false(any(is.na(microorganisms.codes$mo)))
expect_false(any(microorganisms.translation$mo_old %in% microorganisms$mo))
# antibiotic names must always be coercible to their original AB code
expect_identical(antibiotics$ab, as.ab(antibiotics$name))
# there should be no diacritics (i.e. non ASCII) characters in the datasets (CRAN policy)
datasets <- data(package = "AMR", envir = asNamespace("AMR"))$results[, "Item"]
for (i in seq_len(length(datasets))) {
@ -52,6 +52,8 @@ test_that("data sets are valid", {
})
test_that("creation of data sets is valid", {
skip_on_cran()
df <- create_MO_lookup()
expect_lt(nrow(df[which(df$prevalence == 1), ]), nrow(df[which(df$prevalence == 2), ]))
expect_lt(nrow(df[which(df$prevalence == 2), ]), nrow(df[which(df$prevalence == 3), ]))
@ -59,16 +61,18 @@ test_that("creation of data sets is valid", {
"kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies",
"rank", "ref", "species_id", "source", "prevalence", "snomed",
"kingdom_index", "fullname_lower", "g_species") %in% colnames(df)))
olddf <- create_MO.old_lookup()
expect_true(all(c("fullname", "fullname_new", "ref", "prevalence",
"fullname_lower", "g_species") %in% colnames(olddf)))
})
test_that("CoL version info works", {
expect_identical(class(catalogue_of_life_version()),
c("catalogue_of_life_version", "list"))
skip_on_cran()
expect_identical(class(catalogue_of_life_version()),
c("catalogue_of_life_version", "list"))
expect_output(print(catalogue_of_life_version()))
})

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@ -22,6 +22,7 @@
context("deprecated.R")
test_that("deprecated functions work", {
skip_on_cran()
expect_equal(suppressWarnings(portion_S(example_isolates$AMX)), proportion_S(example_isolates$AMX))
expect_equal(suppressWarnings(portion_SI(example_isolates$AMX)), proportion_SI(example_isolates$AMX))
expect_equal(suppressWarnings(portion_I(example_isolates$AMX)), proportion_I(example_isolates$AMX))

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@ -22,6 +22,7 @@
context("disk.R")
test_that("disk works", {
skip_on_cran()
expect_true(as.disk(8) == as.disk("8"))
expect_true(is.disk(as.disk(8)))

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@ -22,7 +22,6 @@
context("first_isolate.R")
test_that("first isolates work", {
skip_on_cran()
# first isolates

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@ -22,6 +22,7 @@
context("g.test.R")
test_that("G-test works", {
skip_on_cran()
# GOODNESS-OF-FIT

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@ -22,6 +22,7 @@
context("get_locale.R")
test_that("get_locale works", {
skip_on_cran()
expect_identical(mo_genus("B_GRAMP", language = "pt"),
"(Gram positivos desconhecidos)")

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@ -25,7 +25,7 @@ test_that("ggplot_rsi works", {
skip_on_cran()
skip_if_not("ggplot2" %in% rownames(installed.packages()))
skip_if_not_installed("ggplot2")
library(dplyr)
library(ggplot2)

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@ -22,6 +22,7 @@
context("guess_ab_col.R")
test_that("guess_ab_col works", {
skip_on_cran()
expect_equal(guess_ab_col(example_isolates, "amox"),
"AMX")

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@ -22,6 +22,7 @@
context("join_microorganisms.R")
test_that("joins work", {
skip_on_cran()
unjoined <- example_isolates
inner <- example_isolates %>% inner_join_microorganisms()
left <- example_isolates %>% left_join_microorganisms()

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@ -22,6 +22,7 @@
context("key_antibiotics.R")
test_that("keyantibiotics work", {
skip_on_cran()
expect_equal(length(key_antibiotics(example_isolates, warnings = FALSE)), nrow(example_isolates))
expect_false(all(is.na(key_antibiotics(example_isolates))))
expect_true(key_antibiotics_equal("SSS", "SSS"))

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@ -22,6 +22,7 @@
context("kurtosis.R")
test_that("kurtosis works", {
skip_on_cran()
expect_equal(kurtosis(example_isolates$age),
3.549319,
tolerance = 0.00001)

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@ -22,6 +22,7 @@
context("like.R")
test_that("`like` works", {
skip_on_cran()
expect_true(sum("test" %like% c("^t", "^s")) == 1)
expect_true("test" %like% "test")
expect_true("test" %like% "TEST")

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@ -22,6 +22,7 @@
context("mic.R")
test_that("mic works", {
skip_on_cran()
expect_true(as.mic(8) == as.mic("8"))
expect_true(as.mic("1") > as.mic("<=0.0625"))
expect_true(as.mic("1") < as.mic(">=32"))

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@ -22,6 +22,7 @@
context("misc.R")
test_that("percentages works", {
skip_on_cran()
expect_equal(percentage(0.25), "25%")
expect_equal(percentage(0.5), "50%")
expect_equal(percentage(0.500, digits = 1), "50.0%")
@ -32,6 +33,7 @@ test_that("percentages works", {
})
test_that("functions missing in older R versions work", {
skip_on_cran()
expect_equal(strrep("A", 5), "AAAAA")
expect_equal(strrep(c("A", "B"), c(5, 2)), c("AAAAA", "BB"))
expect_equal(trimws(" test "), "test")
@ -40,6 +42,7 @@ test_that("functions missing in older R versions work", {
})
test_that("looking up ab columns works", {
skip_on_cran()
expect_warning(generate_warning_abs_missing(c("AMP", "AMX")))
expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))

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@ -1,20 +0,0 @@
# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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. #
# #
# We created this package for both routine data analysis and academic #
# research and it 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.github.io/AMR. #
# ==================================================================== #

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@ -22,6 +22,7 @@
context("p_symbol.R")
test_that("P symbol works", {
skip_on_cran()
expect_identical(p_symbol(c(0.001, 0.01, 0.05, 0.1, 1, NA, 3)),
c("***", "**", "*", ".", " ", NA, NA))
})

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@ -22,6 +22,7 @@
context("resistance_predict.R")
test_that("prediction of rsi works", {
skip_on_cran()
AMX_R <- example_isolates %>%
filter(mo == "B_ESCHR_COLI") %>%
rsi_predict(col_ab = "AMX",

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@ -22,7 +22,6 @@
context("rsi.R")
test_that("rsi works", {
skip_on_cran()
expect_true(as.rsi("S") < as.rsi("I"))

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@ -22,6 +22,7 @@
context("skewness.R")
test_that("skewness works", {
skip_on_cran()
expect_equal(skewness(example_isolates$age),
-0.8958019,
tolerance = 0.00001)