filter_ab_class()
for the filter()
equivalent.
if (require("dplyr")) { +if (FALSE) { + library(dplyr) # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem): example_isolates %>% diff --git a/docs/reference/filter_ab_class.html b/docs/reference/filter_ab_class.html index 18c5fe1f..7659109f 100644 --- a/docs/reference/filter_ab_class.html +++ b/docs/reference/filter_ab_class.html @@ -303,7 +303,8 @@ The lifecycle of this function is stable
antibiotic_class_selectors()
for theselect()
equivalent.Examples
-if (require(dplyr)) { +if (FALSE) { +library(dplyr) # filter on isolates that have any result for any aminoglycoside example_isolates %>% filter_ab_class("aminoglycoside") @@ -332,9 +333,7 @@ The lifecycle of this function is stableexample_isolates %>% filter_aminoglycosides("R", "all") %>% filter_fluoroquinolones("R", "all") -} -if (FALSE) { # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal: example_isolates %>% filter_carbapenems("R", "all") example_isolates %>% filter(across(carbapenems(), ~. == "R")) diff --git a/docs/reference/ggplot_pca.html b/docs/reference/ggplot_pca.html index 6281548c..65b1d481 100644 --- a/docs/reference/ggplot_pca.html +++ b/docs/reference/ggplot_pca.html @@ -388,7 +388,8 @@ The lifecycle of this function is maturing< # See ?example_isolates. # See ?pca for more info about Principal Component Analysis (PCA). -if (require("dplyr")) { +if (FALSE) { + library(dplyr) pca_model <- example_isolates %>% filter(mo_genus(mo) == "Staphylococcus") %>% group_by(species = mo_shortname(mo)) %>% diff --git a/docs/reference/resistance_predict.html b/docs/reference/resistance_predict.html index 8528eb4a..dcd0ebc7 100644 --- a/docs/reference/resistance_predict.html +++ b/docs/reference/resistance_predict.html @@ -411,7 +411,9 @@ A microorganism is categorised as Susceptible, Increased exposure when } # create nice plots with ggplot2 yourself -if (require(ggplot2) & require("dplyr")) { +if (FALSE) { + library(dplyr) + library(ggplot2) data <- example_isolates %>% filter(mo == as.mo("E. coli")) %>% diff --git a/man/ab_from_text.Rd b/man/ab_from_text.Rd index 4ca3413c..569c01af 100644 --- a/man/ab_from_text.Rd +++ b/man/ab_from_text.Rd @@ -80,7 +80,7 @@ ab_from_text("500 mg amoxi po and 400mg cipro iv", collapse = ", ") abx <- ab_from_text("500 mg amoxi po and 400mg cipro iv") ab_group(abx[[1]]) -if (require(dplyr)) { +if (require("dplyr")) { tibble(clinical_text = c("given 400mg cipro and 500 mg amox", "started on doxy iv today")) \%>\% mutate(abx_codes = ab_from_text(clinical_text), diff --git a/man/antibiotic_class_selectors.Rd b/man/antibiotic_class_selectors.Rd index 9317fa1a..be67d356 100644 --- a/man/antibiotic_class_selectors.Rd +++ b/man/antibiotic_class_selectors.Rd @@ -58,7 +58,8 @@ All columns will be searched for known antibiotic names, abbreviations, brand na These functions only work if the \code{tidyselect} package is installed, that comes with the \code{dplyr} package. An error will be thrown if \code{tidyselect} package is not installed, or if the functions are used outside a function that allows Tidyverse selections like \code{select()} or \code{pivot_longer()}. } \examples{ -if (require("dplyr")) { +\dontrun{ + library(dplyr) # this will select columns 'IPM' (imipenem) and 'MEM' (meropenem): example_isolates \%>\% diff --git a/man/filter_ab_class.Rd b/man/filter_ab_class.Rd index 96dcd603..51cc0e85 100644 --- a/man/filter_ab_class.Rd +++ b/man/filter_ab_class.Rd @@ -71,7 +71,8 @@ If the unlying code needs breaking changes, they will occur gradually. For examp } \examples{ -if (require(dplyr)) { +\dontrun{ +library(dplyr) # filter on isolates that have any result for any aminoglycoside example_isolates \%>\% filter_ab_class("aminoglycoside") @@ -100,9 +101,7 @@ example_isolates \%>\% example_isolates \%>\% filter_aminoglycosides("R", "all") \%>\% filter_fluoroquinolones("R", "all") -} -\dontrun{ # with dplyr 1.0.0 and higher (that adds 'across()'), this is equal: example_isolates \%>\% filter_carbapenems("R", "all") example_isolates \%>\% filter(across(carbapenems(), ~. == "R")) diff --git a/man/ggplot_pca.Rd b/man/ggplot_pca.Rd index a822f2c6..15f98a40 100644 --- a/man/ggplot_pca.Rd +++ b/man/ggplot_pca.Rd @@ -118,7 +118,8 @@ The \link[=lifecycle]{lifecycle} of this function is \strong{maturing}. The unly # See ?example_isolates. # See ?pca for more info about Principal Component Analysis (PCA). -if (require("dplyr")) { +\dontrun{ + library(dplyr) pca_model <- example_isolates \%>\% filter(mo_genus(mo) == "Staphylococcus") \%>\% group_by(species = mo_shortname(mo)) \%>\% diff --git a/man/resistance_predict.Rd b/man/resistance_predict.Rd index 8fffc0b0..beb368bb 100644 --- a/man/resistance_predict.Rd +++ b/man/resistance_predict.Rd @@ -150,7 +150,9 @@ if (require("dplyr")) { } # create nice plots with ggplot2 yourself -if (require(ggplot2) & require("dplyr")) { +\dontrun{ + library(dplyr) + library(ggplot2) data <- example_isolates \%>\% filter(mo == as.mo("E. coli")) \%>\% diff --git a/tests/testthat/test-ab.R b/tests/testthat/test-ab.R index 18fa49dc..a3ce9556 100755 --- a/tests/testthat/test-ab.R +++ b/tests/testthat/test-ab.R @@ -22,7 +22,6 @@ context("ab.R") test_that("as.ab works", { - skip_on_cran() expect_equal(as.character(as.ab(c("J01FA01", diff --git a/tests/testthat/test-ab_from_text.R b/tests/testthat/test-ab_from_text.R index eefc472c..17c11c5d 100644 --- a/tests/testthat/test-ab_from_text.R +++ b/tests/testthat/test-ab_from_text.R @@ -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]], diff --git a/tests/testthat/test-ab_property.R b/tests/testthat/test-ab_property.R index 91a39d0f..bbe425f0 100644 --- a/tests/testthat/test-ab_property.R +++ b/tests/testthat/test-ab_property.R @@ -22,7 +22,6 @@ context("ab_property.R") test_that("ab_property works", { - skip_on_cran() expect_identical(ab_name("AMX"), "Amoxicillin") diff --git a/tests/testthat/test-age.R b/tests/testthat/test-age.R index d0f7341a..167a83a8 100644 --- a/tests/testthat/test-age.R +++ b/tests/testthat/test-age.R @@ -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))), diff --git a/tests/testthat/test-availability.R b/tests/testthat/test-availability.R index ec45fd97..134c4b95 100644 --- a/tests/testthat/test-availability.R +++ b/tests/testthat/test-availability.R @@ -22,5 +22,6 @@ context("availability.R") test_that("availability works", { + skip_on_cran() expect_equal(class(availability(example_isolates)), "data.frame") }) diff --git a/tests/testthat/test-bug_drug_combinations.R b/tests/testthat/test-bug_drug_combinations.R index 3cfdfa6b..3dd5dbd9 100644 --- a/tests/testthat/test-bug_drug_combinations.R +++ b/tests/testthat/test-bug_drug_combinations.R @@ -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)) diff --git a/tests/testthat/test-count.R b/tests/testthat/test-count.R index 9dbfa6f4..02ae9173 100644 --- a/tests/testthat/test-count.R +++ b/tests/testthat/test-count.R @@ -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)) diff --git a/tests/testthat/test-data.R b/tests/testthat/test-data.R index 3f01a127..f2a0dbb0 100644 --- a/tests/testthat/test-data.R +++ b/tests/testthat/test-data.R @@ -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$prevalence == 3), ])) @@ -59,16 +61,18 @@ test_that("creation of data sets is valid", { "kingdom", "phylum", "class", "order", "family", "genus", "species", "subspecies", "rank", "ref", "species_id", "source", "prevalence", "snomed", "kingdom_index", "fullname_lower", "g_species") %in% colnames(df))) - + olddf <- create_MO.old_lookup() expect_true(all(c("fullname", "fullname_new", "ref", "prevalence", "fullname_lower", "g_species") %in% colnames(olddf))) - + }) test_that("CoL version info works", { - expect_identical(class(catalogue_of_life_version()), - c("catalogue_of_life_version", "list")) - + skip_on_cran() + + expect_identical(class(catalogue_of_life_version()), + c("catalogue_of_life_version", "list")) + expect_output(print(catalogue_of_life_version())) }) diff --git a/tests/testthat/test-deprecated.R b/tests/testthat/test-deprecated.R index 5fdd2d36..992ec8d5 100644 --- a/tests/testthat/test-deprecated.R +++ b/tests/testthat/test-deprecated.R @@ -22,6 +22,7 @@ context("deprecated.R") test_that("deprecated functions work", { + skip_on_cran() expect_equal(suppressWarnings(portion_S(example_isolates$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)) diff --git a/tests/testthat/test-disk.R b/tests/testthat/test-disk.R index 9c7d6461..48246e23 100755 --- a/tests/testthat/test-disk.R +++ b/tests/testthat/test-disk.R @@ -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))) diff --git a/tests/testthat/test-first_isolate.R b/tests/testthat/test-first_isolate.R index 08270d69..292ce7e2 100755 --- a/tests/testthat/test-first_isolate.R +++ b/tests/testthat/test-first_isolate.R @@ -22,7 +22,6 @@ context("first_isolate.R") test_that("first isolates work", { - skip_on_cran() # first isolates diff --git a/tests/testthat/test-g.test.R b/tests/testthat/test-g.test.R index 35fc17fa..06a6d7e4 100644 --- a/tests/testthat/test-g.test.R +++ b/tests/testthat/test-g.test.R @@ -22,6 +22,7 @@ context("g.test.R") test_that("G-test works", { + skip_on_cran() # GOODNESS-OF-FIT diff --git a/tests/testthat/test-get_locale.R b/tests/testthat/test-get_locale.R index 9180fdfe..e98fa2fb 100644 --- a/tests/testthat/test-get_locale.R +++ b/tests/testthat/test-get_locale.R @@ -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)") diff --git a/tests/testthat/test-ggplot_rsi.R b/tests/testthat/test-ggplot_rsi.R index 7298e203..6214098d 100644 --- a/tests/testthat/test-ggplot_rsi.R +++ b/tests/testthat/test-ggplot_rsi.R @@ -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) diff --git a/tests/testthat/test-guess_ab_col.R b/tests/testthat/test-guess_ab_col.R index d1d59b02..cfbe6606 100644 --- a/tests/testthat/test-guess_ab_col.R +++ b/tests/testthat/test-guess_ab_col.R @@ -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") diff --git a/tests/testthat/test-join_microorganisms.R b/tests/testthat/test-join_microorganisms.R index eeef5bbe..bdda1c62 100755 --- a/tests/testthat/test-join_microorganisms.R +++ b/tests/testthat/test-join_microorganisms.R @@ -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() diff --git a/tests/testthat/test-key_antibiotics.R b/tests/testthat/test-key_antibiotics.R index 463aea5e..578772e7 100644 --- a/tests/testthat/test-key_antibiotics.R +++ b/tests/testthat/test-key_antibiotics.R @@ -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")) diff --git a/tests/testthat/test-kurtosis.R b/tests/testthat/test-kurtosis.R index bb3fd3b9..ebf824ca 100644 --- a/tests/testthat/test-kurtosis.R +++ b/tests/testthat/test-kurtosis.R @@ -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) diff --git a/tests/testthat/test-like.R b/tests/testthat/test-like.R index 7adee61b..1c85033f 100644 --- a/tests/testthat/test-like.R +++ b/tests/testthat/test-like.R @@ -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") diff --git a/tests/testthat/test-mic.R b/tests/testthat/test-mic.R index d9045e84..9b0fac82 100755 --- a/tests/testthat/test-mic.R +++ b/tests/testthat/test-mic.R @@ -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")) diff --git a/tests/testthat/test-misc.R b/tests/testthat/test-misc.R index 62fa1557..c425a501 100755 --- a/tests/testthat/test-misc.R +++ b/tests/testthat/test-misc.R @@ -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")) diff --git a/tests/testthat/test-mo_history.R b/tests/testthat/test-mo_history.R deleted file mode 100644 index 4b7b04a0..00000000 --- a/tests/testthat/test-mo_history.R +++ /dev/null @@ -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. # -# ==================================================================== # diff --git a/tests/testthat/test-p_symbol.R b/tests/testthat/test-p_symbol.R index 7fdcba53..179b6419 100644 --- a/tests/testthat/test-p_symbol.R +++ b/tests/testthat/test-p_symbol.R @@ -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)) }) diff --git a/tests/testthat/test-resistance_predict.R b/tests/testthat/test-resistance_predict.R index fd8f2aaf..e66df7af 100644 --- a/tests/testthat/test-resistance_predict.R +++ b/tests/testthat/test-resistance_predict.R @@ -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", diff --git a/tests/testthat/test-rsi.R b/tests/testthat/test-rsi.R index eaa6a368..11ac1143 100644 --- a/tests/testthat/test-rsi.R +++ b/tests/testthat/test-rsi.R @@ -22,7 +22,6 @@ context("rsi.R") test_that("rsi works", { - skip_on_cran() expect_true(as.rsi("S") < as.rsi("I")) diff --git a/tests/testthat/test-skewness.R b/tests/testthat/test-skewness.R index ad7e413b..2e986840 100644 --- a/tests/testthat/test-skewness.R +++ b/tests/testthat/test-skewness.R @@ -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)