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AMR
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final

This commit is contained in:
dr. M.S. (Matthijs) Berends 2022-10-05 00:11:22 +02:00
parent 4e9de9eb5d
commit cb76b16b69
6 changed files with 9 additions and 9 deletions
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2
.github/workflows/check.yaml vendored
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@ -61,7 +61,7 @@ jobs:
- {os: ubuntu-22.04, r: '4.1', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '4.0', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.6', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.5', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.5.0', allowfail: true, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.4', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.3', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}
- {os: ubuntu-22.04, r: '3.2', allowfail: false, rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest"}

2
.github/workflows/lintr.yaml vendored
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@ -63,7 +63,7 @@ jobs:
# lose deprecated
linters <- linters[!grepl("^(closed_curly|open_curly|paren_brace|semicolon_terminator)_linter$", linters)]
# and the ones we find unnnecessary
linters <- linters[!grepl("^(extraction_operator|implicit_integer|line_length|object_name|nonportable_path)_linter$", linters)]
linters <- linters[!grepl("^(extraction_operator|implicit_integer|line_length|object_name|nonportable_path|is)_linter$", linters)]
# put the functions in a list
linters <- lapply(linters, function(l) eval(parse(text = paste0("lintr::", l, "()")), envir = asNamespace("lintr")))
# run them all!

4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.8.2.9029
Date: 2022-10-04
Version: 1.8.2.9030
Date: 2022-10-05
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9029
# AMR 1.8.2.9030
This version will eventually become v2.0! We're happy to reach a new major milestone soon!

4
inst/tinytest/test-disk.R
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@ -46,11 +46,11 @@ pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.disk(c(10, 20, 40))))
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"))
expect_silent(plot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"))
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(autoplot(as.disk(c(10, 20, 40))), "gg")
expect_inherits(autoplot(as.disk(c(10, 20, 40)), expand = FALSE), "gg")
expect_inherits(autoplot(as.disk(c(10, 20, 40)), mo = "esco", ab = "cipr"), "gg")
expect_inherits(autoplot(as.disk(c(10, 20, 40)), mo = "Escherichia coli", ab = "cipr"), "gg")
}
expect_stdout(print(as.disk(12)))

4
inst/tinytest/test-mic.R
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@ -61,11 +61,11 @@ pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.mic(c(1, 2, 4, 8))))
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"))
expect_silent(plot(as.mic(c(1, 2, 4, 8)), mo = "Escherichia coli", ab = "cipr"))
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8))), "gg")
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8)), expand = FALSE), "gg")
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "esco", ab = "cipr"), "gg")
expect_inherits(autoplot(as.mic(c(1, 2, 4, 8, 32)), mo = "Escherichia coli", ab = "cipr"), "gg")
}
expect_stdout(print(as.mic(c(1, 2, 4, 8))))