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coercion fixes

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dr. M.S. (Matthijs) Berends committed 2022-10-19 06:59:36 +02:00
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commit f203928f7e
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DESCRIPTION
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@@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.8.2.9020 Version: 1.8.2.9021
Date: 2022-10-18 Date: 2022-10-19
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by data analysis and to work with microbial and antimicrobial properties by
NEWS.md
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# AMR 1.8.2.9020 # AMR 1.8.2.9021
This version will eventually become v2.0! We're happy to reach a new major milestone soon! This version will eventually become v2.0! We're happy to reach a new major milestone soon!
R/mo.R
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@@ -440,7 +440,7 @@ as.mo <- function(x,
# All unknowns ---- # All unknowns ----
out[is.na(out) & !is.na(x)] <- "UNKNOWN" out[is.na(out) & !is.na(x)] <- "UNKNOWN"
AMR_env$mo_failures <- unique(x[out == "UNKNOWN" & x != "UNKNOWN" & !is.na(x)]) AMR_env$mo_failures <- unique(x[out == "UNKNOWN" & !x %in% c("UNKNOWN", "con") & !x %like_case% "^[(]unknown [a-z]+[)]$" & !is.na(x)])
if (length(AMR_env$mo_failures) > 0) { if (length(AMR_env$mo_failures) > 0) {
warning_("The following input could not be coerced and was returned as \"UNKNOWN\": ", vector_and(AMR_env$mo_failures, quotes = TRUE), ".\nYou can retrieve this list with `mo_failures()`.") warning_("The following input could not be coerced and was returned as \"UNKNOWN\": ", vector_and(AMR_env$mo_failures, quotes = TRUE), ".\nYou can retrieve this list with `mo_failures()`.")
} }
inst/tinytest/test-ab.R
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@@ -51,7 +51,6 @@ expect_stdout(print(data.frame(a = as.ab("amox"))))
expect_warning(as.ab("J00AA00")) # ATC not yet available in data set expect_warning(as.ab("J00AA00")) # ATC not yet available in data set
expect_warning(as.ab("UNKNOWN")) expect_warning(as.ab("UNKNOWN"))
expect_warning(as.ab(""))
expect_stdout(print(as.ab("amox"))) expect_stdout(print(as.ab("amox")))
@@ -75,7 +74,7 @@ expect_equal(
c("MEM", "AMC") c("MEM", "AMC")
) )
expect_message(as.ab("cipro mero")) expect_warning(as.ab("cipro mero"))
# based on Levenshtein distance # based on Levenshtein distance
expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam") expect_identical(ab_name("ceftazidim/avibactam", language = NULL), "Ceftazidime/avibactam")
@@ -86,6 +85,7 @@ expect_inherits(x[1], "ab")
expect_inherits(x[[1]], "ab") expect_inherits(x[[1]], "ab")
expect_inherits(c(x[1], x[9]), "ab") expect_inherits(c(x[1], x[9]), "ab")
expect_inherits(unique(x[1], x[9]), "ab") expect_inherits(unique(x[1], x[9]), "ab")
expect_inherits(rep(x[1], x[9]), "ab")
expect_warning(x[1] <- "invalid code") expect_warning(x[1] <- "invalid code")
expect_warning(x[[1]] <- "invalid code") expect_warning(x[[1]] <- "invalid code")
expect_warning(c(x[1], "test")) expect_warning(c(x[1], "test"))
inst/tinytest/test-mo.R
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@@ -283,7 +283,7 @@ expect_equal(
) )
# no viruses # no viruses
expect_equal(as.mo("Virus"), as.mo("UNKNOWN")) expect_equal(suppressWarnings(as.mo("Virus")), as.mo("UNKNOWN"))
# summary # summary
expect_equal(length(summary(example_isolates$mo)), 6) expect_equal(length(summary(example_isolates$mo)), 6)