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new SDD and N for as.sir()

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2024-05-20 15:27:04 +02:00
parent b68f47d985
commit 08a27922a8
28 changed files with 225 additions and 172 deletions
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16
inst/tinytest/test-sir.R
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@ -45,14 +45,14 @@ expect_inherits(x[[1]], "sir")
expect_inherits(c(x[1], x[9]), "sir")
expect_inherits(unique(x[1], x[9]), "sir")
pdf(NULL) # prevent Rplots.pdf being created
expect_silent(barplot(as.sir(c("S", "I", "R"))))
expect_silent(plot(as.sir(c("S", "I", "R"))))
expect_silent(barplot(as.sir(c("S", "SDD", "I", "R", "N"))))
expect_silent(plot(as.sir(c("S", "SDD", "I", "R", "N"))))
if (AMR:::pkg_is_available("ggplot2")) {
expect_inherits(ggplot2::autoplot(as.sir(c("S", "I", "R"))), "gg")
expect_inherits(ggplot2::autoplot(as.sir(c("S", "SDD", "I", "R", "N"))), "gg")
}
expect_stdout(print(as.sir(c("S", "I", "R"))))
expect_equal(as.character(as.sir(c(1:3))), c("S", "I", "R"))
expect_equal(as.character(as.sir(c(1:3))), c("S", "I", "R"))
expect_stdout(print(as.sir(c("S", "SDD", "I", "R", "N"))))
expect_equal(as.character(as.sir(c(1:3))), c("S", "SDD", "I", "R", "N"))
expect_equal(as.character(as.sir(c(1:3))), c("S", "SDD", "I", "R", "N"))
expect_equal(suppressWarnings(as.logical(as.sir("INVALID VALUE"))), NA)
expect_equal(
summary(as.sir(c("S", "R"))),
@ -148,7 +148,7 @@ expect_equal(suppressMessages(
guideline = "CLSI 2019"
)
)),
c("S", "S", "I", "R", "R")
c("S", c("S", "SDD", "I", "R", "N"), "R")
)
expect_true(is.data.frame(sir_interpretation_history(clean = FALSE)))
@ -250,7 +250,7 @@ expect_inherits(
expect_inherits(
suppressWarnings(as.sir(data.frame(
mo = "Escherichia coli",
amoxi = c("S", "I", "R", "invalid")
amoxi = c("S", "SDD", "I", "R", "N", "invalid")
))$amoxi),
"sir"
)