-
+
+
Last updated: 13 May 2021
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 105bfeb3..75389aea 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
-last_built: 2021-05-13T19:35Z
+last_built: 2021-05-13T20:43Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles
diff --git a/docs/reference/index.html b/docs/reference/index.html
index c87dd6d3..03e9e9c3 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9027
+ 1.6.0.9028
diff --git a/docs/survey.html b/docs/survey.html
index 3368ca0c..2c068b0d 100644
--- a/docs/survey.html
+++ b/docs/survey.html
@@ -81,7 +81,7 @@
AMR (for R)
- 1.6.0.9027
+ 1.6.0.9028
diff --git a/tests/testthat/test-_misc.R b/tests/testthat/test-_misc.R
index b1b82ab0..5561429e 100755
--- a/tests/testthat/test-_misc.R
+++ b/tests/testthat/test-_misc.R
@@ -51,15 +51,17 @@ test_that("looking up ab columns works", {
expect_warning(generate_warning_abs_missing(c("AMP", "AMX"), any = TRUE))
expect_warning(get_column_abx(example_isolates, hard_dependencies = "FUS"))
expect_message(get_column_abx(example_isolates, soft_dependencies = "FUS"))
- expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
- expect_warning(get_column_abx(dplyr::rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
+ if (suppressWarnings(require("dplyr"))) {
+ expect_warning(get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = TRUE))
+ expect_warning(get_column_abx(rename(example_isolates, thisone = AMX), amox = "thisone", tmp = "thisone", verbose = FALSE))
+ }
})
test_that("looking up ab columns works", {
skip_on_cran()
-
+
# we rely on "grouped_tbl" being a class of grouped tibbles, so implement a test that checks for this:
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_true(is_null_or_grouped_tbl(example_isolates %>% group_by(hospital_id)))
}
diff --git a/tests/testthat/test-ab_class_selectors.R b/tests/testthat/test-ab_class_selectors.R
index bc215db8..a02ff5da 100644
--- a/tests/testthat/test-ab_class_selectors.R
+++ b/tests/testthat/test-ab_class_selectors.R
@@ -28,19 +28,20 @@ context("ab_class_selectors.R")
test_that("Antibiotic class selectors work", {
skip_on_cran()
- expect_lt(example_isolates %>% dplyr::select(aminoglycosides()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(carbapenems()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(cephalosporins()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(cephalosporins_1st()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(cephalosporins_2nd()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(cephalosporins_3rd()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(cephalosporins_4th()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(cephalosporins_5th()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(fluoroquinolones()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(glycopeptides()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(macrolides()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(oxazolidinones()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(penicillins()) %>% ncol(), ncol(example_isolates))
- expect_lt(example_isolates %>% dplyr::select(tetracyclines()) %>% ncol(), ncol(example_isolates))
-
+ if (suppressWarnings(require("dplyr"))) {
+ expect_lt(example_isolates %>% select(aminoglycosides()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(carbapenems()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(cephalosporins()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(cephalosporins_1st()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(cephalosporins_2nd()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(cephalosporins_3rd()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(cephalosporins_4th()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(cephalosporins_5th()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(fluoroquinolones()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(glycopeptides()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(macrolides()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(oxazolidinones()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(penicillins()) %>% ncol(), ncol(example_isolates))
+ expect_lt(example_isolates %>% select(tetracyclines()) %>% ncol(), ncol(example_isolates))
+ }
})
diff --git a/tests/testthat/test-count.R b/tests/testthat/test-count.R
index f60f62ae..fd988c4e 100644
--- a/tests/testthat/test-count.R
+++ b/tests/testthat/test-count.R
@@ -58,7 +58,7 @@ test_that("counts work", {
expect_error(count_df(c("A", "B", "C")))
expect_error(count_df(example_isolates[, "date"]))
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_equal(example_isolates %>% count_susceptible(AMC), 1433)
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = TRUE), 1687)
expect_equal(example_isolates %>% count_susceptible(AMC, GEN, only_all_tested = FALSE), 1764)
diff --git a/tests/testthat/test-disk.R b/tests/testthat/test-disk.R
index 82a94e4d..15bb359d 100755
--- a/tests/testthat/test-disk.R
+++ b/tests/testthat/test-disk.R
@@ -47,14 +47,14 @@ test_that("disk works", {
expect_silent(plot(as.disk(c(10, 20, 40))))
expect_silent(plot(as.disk(c(10, 20, 40)), expand = FALSE))
expect_silent(plot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"))
- if (require("ggplot2")) {
+ if (suppressWarnings(require("ggplot2"))) {
expect_s3_class(ggplot(as.disk(c(10, 20, 40))), "gg")
expect_s3_class(ggplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
expect_s3_class(ggplot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"), "gg")
}
expect_output(print(as.disk(12)))
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_output(print(tibble(d = as.disk(12))))
}
diff --git a/tests/testthat/test-episode.R b/tests/testthat/test-episode.R
index e909cfc9..c7005393 100644
--- a/tests/testthat/test-episode.R
+++ b/tests/testthat/test-episode.R
@@ -41,7 +41,7 @@ test_that("episodes work", {
expect_equal(get_episode(test_df$date, 365),
c(1, 1, 2, 2, 2, 3, 3, 4, 1, 2, 2, 2, 3))
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_identical(test_df %>% group_by(patient_id) %>% mutate(f = is_new_episode(date, 365)) %>% pull(f),
c(TRUE, FALSE, TRUE, FALSE, FALSE, FALSE, TRUE, TRUE, TRUE, TRUE, FALSE, FALSE, TRUE))
diff --git a/tests/testthat/test-eucast_rules.R b/tests/testthat/test-eucast_rules.R
index d9aaaf4d..55c42202 100755
--- a/tests/testthat/test-eucast_rules.R
+++ b/tests/testthat/test-eucast_rules.R
@@ -77,7 +77,7 @@ test_that("EUCAST rules work", {
expect_equal(suppressWarnings(eucast_rules(a, "mo", info = FALSE)), b)
# piperacillin must be R in Enterobacteriaceae when tica is R
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_equal(suppressWarnings(
example_isolates %>%
filter(mo_family(mo) == "Enterobacteriaceae") %>%
@@ -115,7 +115,7 @@ test_that("EUCAST rules work", {
"S")
# also test norf
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_output(suppressWarnings(eucast_rules(example_isolates %>% mutate(NOR = "S", NAL = "S"), info = TRUE)))
}
diff --git a/tests/testthat/test-filter_ab_class.R b/tests/testthat/test-filter_ab_class.R
index 4065bc6b..94f55e43 100644
--- a/tests/testthat/test-filter_ab_class.R
+++ b/tests/testthat/test-filter_ab_class.R
@@ -28,7 +28,7 @@ context("filter_ab_class.R")
test_that("ATC-group filtering works", {
skip_on_cran()
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_gt(example_isolates %>% filter_ab_class("carbapenem") %>% nrow(), 0)
expect_gt(example_isolates %>% filter_aminoglycosides() %>% ncol(), 0)
expect_gt(example_isolates %>% filter_carbapenems() %>% ncol(), 0)
diff --git a/tests/testthat/test-first_isolate.R b/tests/testthat/test-first_isolate.R
index 5cd6aca0..9b673eec 100755
--- a/tests/testthat/test-first_isolate.R
+++ b/tests/testthat/test-first_isolate.R
@@ -121,28 +121,34 @@ test_that("first isolates work", {
col_date = "non-existing col",
col_mo = "mo"))
- require("dplyr")
-
- # if mo is not an mo class, result should be the same
- expect_identical(example_isolates %>%
- mutate(mo = as.character(mo)) %>%
- first_isolate(col_date = "date",
- col_mo = "mo",
- col_patient_id = "patient_id",
- info = FALSE),
- example_isolates %>%
- first_isolate(col_date = "date",
- col_mo = "mo",
- col_patient_id = "patient_id",
- info = FALSE))
-
- # support for WHONET
- expect_message(example_isolates %>%
- select(-patient_id) %>%
- mutate(`First name` = "test",
- `Last name` = "test",
- Sex = "Female") %>%
- first_isolate(info = TRUE))
+ if (suppressWarnings(require("dplyr"))) {
+ # if mo is not an mo class, result should be the same
+ expect_identical(example_isolates %>%
+ mutate(mo = as.character(mo)) %>%
+ first_isolate(col_date = "date",
+ col_mo = "mo",
+ col_patient_id = "patient_id",
+ info = FALSE),
+ example_isolates %>%
+ first_isolate(col_date = "date",
+ col_mo = "mo",
+ col_patient_id = "patient_id",
+ info = FALSE))
+
+ # support for WHONET
+ expect_message(example_isolates %>%
+ select(-patient_id) %>%
+ mutate(`First name` = "test",
+ `Last name` = "test",
+ Sex = "Female") %>%
+ first_isolate(info = TRUE))
+
+ # groups
+ x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate())
+ y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.))
+ expect_identical(x, y)
+
+ }
# missing dates should be no problem
df <- example_isolates
@@ -185,10 +191,4 @@ test_that("first isolates work", {
# only one isolate, so return fast
expect_true(first_isolate(data.frame(mo = "Escherichia coli", date = Sys.Date(), patient = "patient"), info = TRUE))
-
- # groups
- x <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate())
- y <- example_isolates %>% group_by(ward_icu) %>% mutate(first = first_isolate(.))
- expect_identical(x, y)
-
})
diff --git a/tests/testthat/test-ggplot_rsi.R b/tests/testthat/test-ggplot_rsi.R
index 5ce82c08..67be05b4 100644
--- a/tests/testthat/test-ggplot_rsi.R
+++ b/tests/testthat/test-ggplot_rsi.R
@@ -32,7 +32,7 @@ test_that("ggplot_rsi works", {
skip_if_not_installed("ggplot2")
skip_if_not_installed("dplyr")
- if (require("dplyr") & require("ggplot2")) {
+ if (suppressWarnings(require("dplyr")) & suppressWarnings(require("ggplot2"))) {
pdf(NULL) # prevent Rplots.pdf being created
diff --git a/tests/testthat/test-mdro.R b/tests/testthat/test-mdro.R
index 838a9cd6..e17141b5 100755
--- a/tests/testthat/test-mdro.R
+++ b/tests/testthat/test-mdro.R
@@ -244,7 +244,7 @@ test_that("mdro works", {
info = FALSE))
# print groups
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), info = TRUE))
expect_output(x <- mdro(example_isolates %>% group_by(hospital_id), guideline = custom, info = TRUE))
}
diff --git a/tests/testthat/test-mic.R b/tests/testthat/test-mic.R
index d4afad7b..2144a4d4 100755
--- a/tests/testthat/test-mic.R
+++ b/tests/testthat/test-mic.R
@@ -53,7 +53,7 @@ test_that("mic works", {
expect_silent(plot(as.mic(c(1, 2, 4, 8))))
expect_silent(plot(as.mic(c(1, 2, 4, 8)), expand = FALSE))
expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "esco", ab = "cipr"))
- if (require("ggplot2")) {
+ if (suppressWarnings(require("ggplot2"))) {
expect_s3_class(ggplot(as.mic(c(1, 2, 4, 8))), "gg")
expect_s3_class(ggplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
expect_s3_class(ggplot(as.mic(c(1, 2, 4, 8, 32)), mo = "esco", ab = "cipr"), "gg")
@@ -62,7 +62,7 @@ test_that("mic works", {
expect_s3_class(summary(as.mic(c(2, 8))), c("summaryDefault", "table"))
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_output(print(tibble(m = as.mic(2:4))))
}
})
diff --git a/tests/testthat/test-mo.R b/tests/testthat/test-mo.R
index 7afb945d..c1e8a144 100644
--- a/tests/testthat/test-mo.R
+++ b/tests/testthat/test-mo.R
@@ -150,7 +150,7 @@ test_that("as.mo works", {
expect_identical(as.character(as.mo("S. salivarius", Lancefield = FALSE)), "B_STRPT_SLVR")
expect_identical(as.character(as.mo("S. salivarius", Lancefield = TRUE)), "B_STRPT_GRPK") # group K
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
# select with one column
expect_identical(
example_isolates[1:10, ] %>%
@@ -282,8 +282,10 @@ test_that("as.mo works", {
expect_equal(suppressWarnings(as.character(as.mo(c("yeasts", "fungi")))),
c("F_YEAST", "F_FUNGUS"))
- # print tibble
- expect_output(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
+ if (suppressWarnings(require("dplyr"))) {
+ # print tibble
+ expect_output(print(tibble(mo = as.mo("B_ESCHR_COLI"))))
+ }
# assigning and subsetting
x <- example_isolates$mo
@@ -299,7 +301,7 @@ test_that("as.mo works", {
c("B_ESCHR_COLI", NA))
# frequency tables
- if (require("cleaner")) {
+ if (suppressWarnings(require("cleaner"))) {
expect_s3_class(cleaner::freq(example_isolates$mo), "freq")
}
diff --git a/tests/testthat/test-mo_property.R b/tests/testthat/test-mo_property.R
index c7b338c8..29c61533 100644
--- a/tests/testthat/test-mo_property.R
+++ b/tests/testthat/test-mo_property.R
@@ -131,7 +131,7 @@ test_that("mo_property works", {
expect_equal(mo_name("test", reference_df = data.frame(col1 = "test", mo = "B_ESCHR_COLI")),
"Escherichia coli")
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_equal(example_isolates %>% filter(mo_is_gram_negative()) %>% nrow(),
730)
expect_equal(example_isolates %>% filter(mo_is_gram_positive()) %>% nrow(),
diff --git a/tests/testthat/test-pca.R b/tests/testthat/test-pca.R
index f1feef64..0475165e 100644
--- a/tests/testthat/test-pca.R
+++ b/tests/testthat/test-pca.R
@@ -49,10 +49,12 @@ test_that("PCA works", {
expect_s3_class(pca_model, "pca")
pdf(NULL) # prevent Rplots.pdf being created
- ggplot_pca(pca_model, ellipse = TRUE)
- ggplot_pca(pca_model, arrows_textangled = FALSE)
+ if (suppressWarnings(require("ggplot2"))) {
+ ggplot_pca(pca_model, ellipse = TRUE)
+ ggplot_pca(pca_model, arrows_textangled = FALSE)
+ }
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
resistance_data <- example_isolates %>%
group_by(order = mo_order(mo),
genus = mo_genus(mo)) %>%
@@ -60,7 +62,9 @@ test_that("PCA works", {
pca_result <- resistance_data %>%
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, "SXT")
expect_s3_class(pca_result, "prcomp")
- ggplot_pca(pca_result, ellipse = TRUE)
- ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
+ if (suppressWarnings(require("ggplot2"))) {
+ ggplot_pca(pca_result, ellipse = TRUE)
+ ggplot_pca(pca_result, ellipse = FALSE, arrows_textangled = FALSE, scale = FALSE)
+ }
}
})
diff --git a/tests/testthat/test-proportion.R b/tests/testthat/test-proportion.R
index 987c1fa0..5949fa7c 100755
--- a/tests/testthat/test-proportion.R
+++ b/tests/testthat/test-proportion.R
@@ -52,7 +52,7 @@ test_that("proportions works", {
0.9382647,
tolerance = 0.0001)
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
# percentages
expect_equal(example_isolates %>%
group_by(hospital_id) %>%
diff --git a/tests/testthat/test-resistance_predict.R b/tests/testthat/test-resistance_predict.R
index e66bdd6b..87041d80 100644
--- a/tests/testthat/test-resistance_predict.R
+++ b/tests/testthat/test-resistance_predict.R
@@ -28,7 +28,7 @@ context("resistance_predict.R")
test_that("prediction of rsi works", {
skip_on_cran()
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_output(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 e70829ed..d51eaf57 100644
--- a/tests/testthat/test-rsi.R
+++ b/tests/testthat/test-rsi.R
@@ -42,7 +42,7 @@ test_that("rsi works", {
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.rsi(c("S", "I", "R"))))
expect_silent(plot(as.rsi(c("S", "I", "R"))))
- if (require("ggplot2")) expect_s3_class(ggplot(as.rsi(c("S", "I", "R"))), "gg")
+ if (suppressWarnings(require("ggplot2"))) expect_s3_class(ggplot(as.rsi(c("S", "I", "R"))), "gg")
expect_output(print(as.rsi(c("S", "I", "R"))))
expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
@@ -64,7 +64,7 @@ test_that("rsi works", {
expect_error(get_guideline("this one does not exist"))
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
# 40 rsi columns
expect_equal(example_isolates %>%
mutate_at(vars(PEN:RIF), as.character) %>%
@@ -77,10 +77,10 @@ test_that("rsi works", {
expect_output(print(tibble(ab = as.rsi("S"))))
}
- if (require("skimr")) {
+ if (suppressWarnings(require("skimr"))) {
expect_s3_class(skim(example_isolates),
"data.frame")
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_s3_class(example_isolates %>%
mutate(m = as.mic(2),
d = as.disk(20)) %>%
@@ -116,7 +116,7 @@ test_that("mic2rsi works", {
expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
as.rsi("R"))
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_true(suppressWarnings(example_isolates %>%
mutate(amox_mic = as.mic(2)) %>%
select(mo, amox_mic) %>%
@@ -149,7 +149,7 @@ test_that("disk2rsi works", {
guideline = "CLSI")),
"R")
- if (require("dplyr")) {
+ if (suppressWarnings(require("dplyr"))) {
expect_true(example_isolates %>%
mutate(amox_disk = as.disk(15)) %>%
select(mo, amox_disk) %>%
@@ -159,7 +159,7 @@ test_that("disk2rsi works", {
}
# frequency tables
- if (require("cleaner")) {
+ if (suppressWarnings(require("cleaner"))) {
expect_s3_class(cleaner::freq(example_isolates$AMX), "freq")
}
})
diff --git a/tests/testthat/test-zzz.R b/tests/testthat/test-zzz.R
index 6e8dcc2c..3891d353 100644
--- a/tests/testthat/test-zzz.R
+++ b/tests/testthat/test-zzz.R
@@ -109,7 +109,9 @@ test_that("imports work", {
fn <- names(import_functions)[i]
pkg <- unname(import_functions[i])
# function should exist in foreign pkg namespace
- expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
- failure_message = paste0("Function ", pkg, "::", fn, "() does not exist anymore"))
+ if (pkg %in% rownames(installed.packages())) {
+ expect(!is.null(import_fn(name = fn, pkg = pkg, error_on_fail = FALSE)),
+ failure_message = paste0("Function ", pkg, "::", fn, "() does not exist anymore"))
+ }
}
})