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AMR
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coercion fixes

This commit is contained in:
dr. M.S. (Matthijs) Berends 2022-10-19 06:59:36 +02:00
parent 3fc39198d0
commit f203928f7e
5 changed files with 7 additions and 7 deletions
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4
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

2
NEWS.md
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@ -1,4 +1,4 @@
# 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!

2
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()`.")
} }

4
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"))

2
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)