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(v1.6.0.9055) support codecov again

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-05-21 20:20:51 +02:00
parent fecc5d183c
commit b210f1327c
72 changed files with 203 additions and 216 deletions
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14
inst/tinytest/test-rsi.R
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@@ -34,7 +34,7 @@ expect_inherits(unique(x[1], x[9]), "rsi")
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 (pkg_is_available("ggplot2")) expect_inherits(ggplot(as.rsi(c("S", "I", "R"))), "gg")
if (AMR:::pkg_is_available("ggplot2")) expect_inherits(ggplot(as.rsi(c("S", "I", "R"))), "gg")
expect_stdout(print(as.rsi(c("S", "I", "R"))))
expect_equal(as.character(as.rsi(c(1:3))), c("S", "I", "R"))
expect_equal(suppressWarnings(as.logical(as.rsi("INVALID VALUE"))), NA)
@@ -49,7 +49,7 @@ expect_identical(as.logical(lapply(example_isolates, is.rsi.eligible)),
expect_error(as.rsi.mic(as.mic(16)))
expect_error(as.rsi.disk(as.disk(16)))
expect_error(get_guideline("this one does not exist"))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
# 40 rsi columns
expect_equal(example_isolates %>%
mutate_at(vars(PEN:RIF), as.character) %>%
@@ -61,10 +61,10 @@ if (pkg_is_available("dplyr")) {
expect_stdout(print(tibble(ab = as.rsi("S"))))
}
if (pkg_is_available("skimr")) {
if (AMR:::pkg_is_available("skimr")) {
expect_inherits(skim(example_isolates),
"data.frame")
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_inherits(example_isolates %>%
mutate(m = as.mic(2),
d = as.disk(20)) %>%
@@ -94,7 +94,7 @@ expect_equal(as.rsi(as.mic(2), "E. coli", "ampicillin", guideline = "EUCAST 2020
as.rsi("S"))
expect_equal(as.rsi(as.mic(32), "E. coli", "ampicillin", guideline = "EUCAST 2020"),
as.rsi("R"))
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_true(suppressWarnings(example_isolates %>%
mutate(amox_mic = as.mic(2)) %>%
select(mo, amox_mic) %>%
@@ -121,7 +121,7 @@ expect_equal(as.character(
ab = "ERY",
guideline = "CLSI")),
"R")
if (pkg_is_available("dplyr")) {
if (AMR:::pkg_is_available("dplyr")) {
expect_true(example_isolates %>%
mutate(amox_disk = as.disk(15)) %>%
select(mo, amox_disk) %>%
@@ -130,7 +130,7 @@ if (pkg_is_available("dplyr")) {
is.rsi())
}
# frequency tables
if (pkg_is_available("cleaner")) {
if (AMR:::pkg_is_available("cleaner")) {
expect_inherits(cleaner::freq(example_isolates$AMX), "freq")
}