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(v1.8.0.9002) as.rsi() cleanup, more informative warnings

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-03-02 15:38:55 +01:00
parent 18e8525d10
commit 3b2b2be5f8
35 changed files with 267 additions and 320 deletions
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7
inst/tinytest/test-mo.R
View File

@ -87,8 +87,9 @@ expect_identical(
"Sthafilokkockus aureeuzz",
"Staphylococcus aureus",
"MRSA",
"VISA")))),
rep("B_STPHY_AURS", 9))
"VISA",
"meth.-resis. S. aureus (MRSA)")))),
rep("B_STPHY_AURS", 10))
expect_identical(
as.character(
as.mo(c("EHEC", "EPEC", "EIEC", "STEC", "ATEC", "UPEC"))),
@ -243,7 +244,7 @@ expect_stdout(print(mo_uncertainties()))
expect_equal(suppressMessages(as.mo(c("Salmonella Goettingen", "Salmonella Typhimurium", "Salmonella Group A"))),
as.mo(c("Salmonella enterica", "Salmonella enterica", "Salmonella")))
# no virusses
# no viruses
expect_equal(as.character(as.mo("Virus")), NA_character_)
# summary

2
inst/tinytest/test-rsi.R
View File

@ -39,6 +39,7 @@ if (AMR:::pkg_is_available("ggplot2")) {
}
expect_stdout(print(as.rsi(c("S", "I", "R"))))
expect_equal(as.character(as.rsi(c(1:3))), 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)
expect_equal(summary(as.rsi(c("S", "R"))),
structure(c("Class" = "rsi",
@ -75,6 +76,7 @@ if (AMR:::pkg_is_available("skimr", min_version = "2.0.0")) {
}
}
expect_equal(as.rsi(c("", "-", NA, "NULL")), c(NA_rsi_, NA_rsi_, NA_rsi_, NA_rsi_))
# S. pneumoniae/ampicillin in EUCAST 2020: 0.5-2 ug/ml (R is only > 2)
expect_equal(as.character(