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

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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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4
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.8.0.9001
Date: 2022-02-26
Version: 1.8.0.9002
Date: 2022-03-02
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

5
NEWS.md
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@ -1,5 +1,5 @@
# `AMR` 1.8.0.9001
## <small>Last updated: 26 February 2022</small>
# `AMR` 1.8.0.9002
## <small>Last updated: 2 March 2022</small>
All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
@ -10,6 +10,7 @@ All functions in this package are considered to be stable. Updates to the AMR in
mo_name("methicillin-resistant S. aureus (MRSA)")
#> [1] "Staphylococcus aureus"
```
* More informative warning messages
### Other
* Fix for unit testing on R 3.3

6
R/aa_helper_functions.R
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@ -206,7 +206,7 @@ check_dataset_integrity <- function() {
" overwritten by your global environment and prevent", plural[2],
" the AMR package from working correctly: ",
vector_and(overwritten, quotes = "'"),
".\nPlease rename your object", plural[3], ".", call = FALSE)
".\nPlease rename your object", plural[3], ".")
}
}
# check if other packages did not overwrite our data sets
@ -492,7 +492,7 @@ message_ <- function(...,
warning_ <- function(...,
add_fn = list(),
immediate = FALSE,
call = TRUE) {
call = FALSE) {
warning(word_wrap(...,
add_fn = add_fn,
as_note = FALSE),
@ -559,7 +559,7 @@ stop_ifnot <- function(expr, ..., call = TRUE) {
return_after_integrity_check <- function(value, type, check_vector) {
if (!all(value[!is.na(value)] %in% check_vector)) {
warning_(paste0("invalid ", type, ", NA generated"), call = FALSE)
warning_(paste0("invalid ", type, ", NA generated"))
value[!value %in% check_vector] <- NA
}
value

10
R/ab.R
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@ -455,15 +455,13 @@ as.ab <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
x_unknown_ATCs <- x_unknown[x_unknown %like% "[A-Z][0-9][0-9][A-Z][A-Z][0-9][0-9]"]
x_unknown <- x_unknown[!x_unknown %in% x_unknown_ATCs]
if (length(x_unknown_ATCs) > 0 & fast_mode == FALSE) {
warning_("These ATC codes are not (yet) in the antibiotics data set: ",
vector_and(x_unknown_ATCs), ".",
call = FALSE)
warning_("in `as.ab()`: these ATC codes are not (yet) in the antibiotics data set: ",
vector_and(x_unknown_ATCs), ".")
}
if (length(x_unknown) > 0 & fast_mode == FALSE) {
warning_("These values could not be coerced to a valid antimicrobial ID: ",
vector_and(x_unknown), ".",
call = FALSE)
warning_("in `as.ab()`: these values could not be coerced to a valid antimicrobial ID: ",
vector_and(x_unknown), ".")
}
x_result <- x_new[match(x_bak_clean, x)]

19
R/ab_property.R
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@ -240,8 +240,8 @@ ab_ddd <- function(x, administration = "oral", ...) {
units <- list(...)$units
if (!is.null(units) && isTRUE(units)) {
if (message_not_thrown_before("ab_ddd", entire_session = TRUE)) {
warning_("Using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead. ",
"This warning will be shown once per session.", call = FALSE)
warning_("in `ab_ddd()`: using `ab_ddd(..., units = TRUE)` is deprecated, use `ab_ddd_units()` to retrieve units instead.",
"This warning will be shown once per session.")
}
ddd_prop <- paste0(ddd_prop, "_units")
} else {
@ -250,9 +250,9 @@ ab_ddd <- function(x, administration = "oral", ...) {
out <- ab_validate(x = x, property = ddd_prop)
if (any(ab_name(x, language = NULL) %like% "/" & is.na(out))) {
warning_("DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package. ",
warning_("in `ab_ddd()`: DDDs of some combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
"www.whocc.no/ddd/list_of_ddds_combined_products/")
}
out
}
@ -265,9 +265,9 @@ ab_ddd_units <- function(x, administration = "oral", ...) {
x <- as.ab(x, ...)
if (any(ab_name(x, language = NULL) %like% "/")) {
warning_("DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package. ",
warning_("in `ab_ddd_units()`: DDDs of combined products are available for different dose combinations and not (yet) part of the AMR package.",
"Please refer to the WHOCC website:\n",
"www.whocc.no/ddd/list_of_ddds_combined_products/", call = FALSE)
"www.whocc.no/ddd/list_of_ddds_combined_products/")
}
ddd_prop <- paste0(administration, "_units")
@ -311,12 +311,12 @@ ab_url <- function(x, open = FALSE, ...) {
NAs <- ab_name(ab, tolower = TRUE, language = NULL)[!is.na(ab) & is.na(atcs)]
if (length(NAs) > 0) {
warning_("No ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
warning_("in `ab_url()`: no ATC code available for ", vector_and(NAs, quotes = FALSE), ".")
}
if (open == TRUE) {
if (length(u) > 1 & !is.na(u[1L])) {
warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
warning_("in `ab_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
}
if (!is.na(u[1L])) {
utils::browseURL(u[1L])
@ -385,7 +385,8 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
},
USE.NAMES = FALSE)
if (any(x %in% c("", NA))) {
warning_("No ", property, " found for column(s): ", vector_and(vars[x %in% c("", NA)], sort = FALSE), call = FALSE)
warning_("in `set_ab_names()`: no ", property, " found for column(s): ",
vector_and(vars[x %in% c("", NA)], sort = FALSE))
x[x %in% c("", NA)] <- vars[x %in% c("", NA)]
}

5
R/ab_selectors.R
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@ -481,14 +481,13 @@ ab_select_exec <- function(function_name,
untreatable <- antibiotics[which(antibiotics$name %like% "-high|EDTA|polysorbate|macromethod|screening|/nacubactam"), "ab", drop = TRUE]
if (any(untreatable %in% names(ab_in_data))) {
if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
warning_("Some agents in `", function_name, "()` were ignored since they cannot be used for treating patients: ",
warning_("in `", function_name, "()`: some agents were ignored since they cannot be used for treating patients: ",
vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
language = NULL,
tolower = TRUE),
quotes = FALSE,
sort = TRUE), ". They can be included using `", function_name, "(only_treatable = FALSE)`. ",
"This warning will be shown once per session.",
call = FALSE)
"This warning will be shown once per session.")
}
ab_in_data <- ab_in_data[!names(ab_in_data) %in% untreatable]
}

6
R/age.R
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@ -95,10 +95,10 @@ age <- function(x, reference = Sys.Date(), exact = FALSE, na.rm = FALSE, ...) {
if (any(ages < 0, na.rm = TRUE)) {
ages[!is.na(ages) & ages < 0] <- NA
warning_("NAs introduced for ages below 0.", call = TRUE)
warning_("in `age()`: NAs introduced for ages below 0.")
}
if (any(ages > 120, na.rm = TRUE)) {
warning_("Some ages are above 120.", call = TRUE)
warning_("in `age()`: some ages are above 120.")
}
if (isTRUE(na.rm)) {
@ -171,7 +171,7 @@ age_groups <- function(x, split_at = c(12, 25, 55, 75), na.rm = FALSE) {
if (any(x < 0, na.rm = TRUE)) {
x[x < 0] <- NA
warning_("NAs introduced for ages below 0.", call = TRUE)
warning_("in `age_groups()`: NAs introduced for ages below 0.")
}
if (is.character(split_at)) {
split_at <- split_at[1L]

2
R/atc_online.R
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@ -175,7 +175,7 @@ atc_online_property <- function(atc_code,
colnames(out) <- gsub("^atc.*", "atc", tolower(colnames(out)))
if (length(out) == 0) {
warning_("ATC not found: ", atc_code[i], ". Please check ", atc_url, ".", call = FALSE)
warning_("in `atc_online_property()`: ATC not found: ", atc_code[i], ". Please check ", atc_url, ".")
returnvalue[i] <- NA
next
}

2
R/bug_drug_combinations.R
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@ -184,7 +184,7 @@ format.bug_drug_combinations <- function(x,
if (inherits(x, "grouped")) {
# bug_drug_combinations() has been run on groups, so de-group here
warning_("formatting the output of `bug_drug_combinations()` does not support grouped variables, they are ignored", call = FALSE)
warning_("in `format()`: formatting the output of `bug_drug_combinations()` does not support grouped variables, they were ignored")
idx <- split(seq_len(nrow(x)), paste0(x$mo, "%%", x$ab))
x <- data.frame(mo = gsub("(.*)%%(.*)", "\\1", names(idx)),
ab = gsub("(.*)%%(.*)", "\\2", names(idx)),

4
R/disk.R
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@ -100,10 +100,10 @@ as.disk <- function(x, na.rm = FALSE) {
unique() %pm>%
sort() %pm>%
vector_and(quotes = TRUE)
warning_(na_after - na_before, " results truncated (",
warning_("in `as.disk()`: ", na_after - na_before, " results truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid disk zones: ",
list_missing, call = FALSE)
list_missing)
}
}
set_clean_class(as.integer(x),

16
R/eucast_rules.R
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@ -181,8 +181,7 @@ eucast_rules <- function(x,
meet_criteria(custom_rules, allow_class = "custom_eucast_rules", allow_NULL = TRUE)
if ("custom" %in% rules & is.null(custom_rules)) {
warning_("No custom rules were set with the `custom_rules` argument",
call = FALSE,
warning_("in `eucast_rules()`: no custom rules were set with the `custom_rules` argument",
immediate = TRUE)
rules <- rules[rules != "custom"]
if (length(rules) == 0) {
@ -915,13 +914,12 @@ eucast_rules <- function(x,
# take order from original data set
warn_lacking_rsi_class <- warn_lacking_rsi_class[order(colnames(x.bak))]
warn_lacking_rsi_class <- warn_lacking_rsi_class[!is.na(warn_lacking_rsi_class)]
warning_("Not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
warning_("in `eucast_rules()`: not all columns with antimicrobial results are of class <rsi>. Transform them on beforehand, with e.g.:\n",
" - ", x_deparsed, " %>% as.rsi(", ifelse(length(warn_lacking_rsi_class) == 1,
warn_lacking_rsi_class,
paste0(warn_lacking_rsi_class[1], ":", warn_lacking_rsi_class[length(warn_lacking_rsi_class)])), ")\n",
" - ", x_deparsed, " %>% mutate_if(is.rsi.eligible, as.rsi)\n",
" - ", x_deparsed, " %>% mutate(across(where(is.rsi.eligible), as.rsi))",
call = FALSE)
" - ", x_deparsed, " %>% mutate(across(where(is.rsi.eligible), as.rsi))")
}
# Return data set ---------------------------------------------------------
@ -986,14 +984,14 @@ edit_rsi <- function(x,
TRUE
})
suppressWarnings(new_edits[rows, cols] <<- to)
warning_("Value \"", to, "\" added to the factor levels of column", ifelse(length(cols) == 1, "", "s"),
warning_("in `eucast_rules()`: value \"", to, "\" added to the factor levels of column",
ifelse(length(cols) == 1, "", "s"),
" ", vector_and(cols, quotes = "`", sort = FALSE),
" because this value was not an existing factor level.",
call = FALSE)
" because this value was not an existing factor level.")
txt_warning()
warned <- FALSE
} else {
warning_(w$message, call = FALSE)
warning_("in `eucast_rules()`: ", w$message)
txt_warning()
}
},

4
R/guess_ab_col.R
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@ -267,7 +267,6 @@ get_column_abx <- function(x,
", as it is already set for ",
names(already_set_as), " (", ab_name(names(already_set_as), tolower = TRUE, language = NULL), ")"),
add_fn = font_red,
call = FALSE,
immediate = verbose)
}
}
@ -338,6 +337,5 @@ generate_warning_abs_missing <- function(missing, any = FALSE) {
}
warning_(paste0("Introducing NAs since", any_txt[1], " these antimicrobials ", any_txt[2], " required: ",
vector_and(missing, quotes = FALSE)),
immediate = TRUE,
call = FALSE)
immediate = TRUE)
}

2
R/join_microorganisms.R
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@ -170,7 +170,7 @@ join_microorganisms <- function(type, x, by, suffix, ...) {
}
if (type %like% "full|left|right|inner" && NROW(joined) > NROW(x)) {
warning_("The newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.", call = FALSE)
warning_("in `", type, "_join()`: the newly joined data set contains ", nrow(joined) - nrow(x), " rows more than the number of rows of `x`.")
}
joined

10
R/key_antimicrobials.R
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@ -150,7 +150,7 @@ key_antimicrobials <- function(x = NULL,
col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
}
if (is.null(col_mo)) {
warning_("No column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`", call = FALSE)
warning_("in `key_antimicrobials()`: no column found for `col_mo`, ignoring antibiotics set in `gram_negative` and `gram_positive`, and antimycotics set in `antifungal`")
gramstain <- NA_character_
kingdom <- NA_character_
} else {
@ -172,11 +172,11 @@ key_antimicrobials <- function(x = NULL,
if (values_new_length < values_old_length &
any(filter, na.rm = TRUE) &
message_not_thrown_before("key_antimicrobials", name)) {
warning_(ifelse(values_new_length == 0,
warning_("in `key_antimicrobials()`: ",
ifelse(values_new_length == 0,
"No columns available ",
paste0("Only using ", values_new_length, " out of ", values_old_length, " defined columns ")),
"as key antimicrobials for ", name, "s. See ?key_antimicrobials.",
call = FALSE)
"as key antimicrobials for ", name, "s. See ?key_antimicrobials.")
}
generate_antimcrobials_string(x[which(filter), c(universal, values), drop = FALSE])
@ -217,7 +217,7 @@ key_antimicrobials <- function(x = NULL,
cols = cols)
if (length(unique(key_ab)) == 1) {
warning_("No distinct key antibiotics determined.", call = FALSE)
warning_("in `key_antimicrobials()`: no distinct key antibiotics determined.")
}
key_ab

8
R/mdro.R
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@ -240,7 +240,7 @@ mdro <- function(x = NULL,
}
if (!is.null(list(...)$country)) {
warning_("Using `country` is deprecated, use `guideline` instead. See ?mdro.", call = FALSE)
warning_("in `mdro()`: using `country` is deprecated, use `guideline` instead. See ?mdro")
guideline <- list(...)$country
}
@ -1550,8 +1550,8 @@ mdro <- function(x = NULL,
if (guideline$code == "cmi2012") {
if (any(x$MDRO == -1, na.rm = TRUE)) {
if (message_not_thrown_before("mdro", "availability")) {
warning_("NA introduced for isolates where the available percentage of antimicrobial classes was below ",
percentage(pct_required_classes), " (set with `pct_required_classes`)", call = FALSE)
warning_("in `mdro()`: NA introduced for isolates where the available percentage of antimicrobial classes was below ",
percentage(pct_required_classes), " (set with `pct_required_classes`)")
}
# set these -1s to NA
x[which(x$MDRO == -1), "MDRO"] <- NA_integer_
@ -1709,7 +1709,7 @@ run_custom_mdro_guideline <- function(df, guideline, info) {
return("error")
})
if (identical(qry, "error")) {
warning_("in custom_mdro_guideline(): rule ", i,
warning_("in `custom_mdro_guideline()`: rule ", i,
" (`", as.character(guideline[[i]]$query), "`) was ignored because of this error message: ",
pkg_env$err_msg,
call = FALSE,

4
R/mic.R
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@ -175,7 +175,7 @@ as.mic <- function(x, na.rm = FALSE) {
unique() %pm>%
sort() %pm>%
vector_and(quotes = TRUE)
warning_(na_after - na_before, " results truncated (",
warning_("in `as.mic()`: ", na_after - na_before, " results truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid MICs: ",
list_missing, call = FALSE)
@ -358,7 +358,7 @@ sort.mic <- function(x, decreasing = FALSE, ...) {
#' @export
#' @noRd
hist.mic <- function(x, ...) {
warning_("Use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values", call = FALSE)
warning_("in `hist()`: use `plot()` or ggplot2's `autoplot()` for optimal plotting of MIC values")
hist(log2(x))
}

47
R/mo.R
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@ -1489,9 +1489,8 @@ exec_as.mo <- function(x,
"You can also use your own reference data with set_mo_source() or directly, e.g.:\n",
' as.mo("mycode", reference_df = data.frame(own = "mycode", mo = "', MO_lookup$mo[match("Escherichia coli", MO_lookup$fullname)], '"))\n',
' mo_name("mycode", reference_df = data.frame(own = "mycode", mo = "', MO_lookup$mo[match("Escherichia coli", MO_lookup$fullname)], '"))\n')
warning_(paste0("\n", msg),
warning_(paste0("\nin `as.mo()`: ", msg),
add_fn = font_red,
call = FALSE,
immediate = TRUE) # thus will always be shown, even if >= warnings
}
# handling uncertainties ----
@ -1531,12 +1530,11 @@ exec_as.mo <- function(x,
# comment below code if all staphylococcal species are categorised as CoNS/CoPS
if (any(x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property])) {
if (message_not_thrown_before("as.mo", "becker")) {
warning_("Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
warning_("in `as.mo()`: Becker ", font_italic("et al."), " (2014, 2019, 2020) does not contain these species named after their publication: ",
font_italic(paste("S.",
sort(mo_species(unique(x[x %in% MO_lookup[which(MO_lookup$species %in% post_Becker), property]]))),
collapse = ", ")),
". Categorisation to CoNS/CoPS was taken from the original scientific publication(s).",
call = FALSE,
immediate = TRUE)
}
}
@ -1709,8 +1707,7 @@ pillar_shaft.mo <- function(x, ...) {
col <- "The data"
}
warning_(col, " contains old MO codes (from a previous AMR package version). ",
"Please update your MO codes with `as.mo()`.",
call = FALSE)
"Please update your MO codes with `as.mo()`.")
}
# make it always fit exactly
@ -1784,8 +1781,7 @@ print.mo <- function(x, print.shortnames = FALSE, ...) {
names(x) <- x_names
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
warning_("Some MO codes are from a previous AMR package version. ",
"Please update these MO codes with `as.mo()`.",
call = FALSE)
"Please update the MO codes with `as.mo()`.")
}
print.default(x, quote = FALSE)
}
@ -1814,8 +1810,7 @@ summary.mo <- function(object, ...) {
as.data.frame.mo <- function(x, ...) {
if (!all(x[!is.na(x)] %in% MO_lookup$mo)) {
warning_("The data contains old MO codes (from a previous AMR package version). ",
"Please update your MO codes with `as.mo()`.",
call = FALSE)
"Please update your MO codes with `as.mo()`.")
}
nm <- deparse1(substitute(x))
if (!"nm" %in% names(list(...))) {
@ -2119,24 +2114,22 @@ replace_old_mo_codes <- function(x, property) {
n_unique <- ""
}
if (property != "mo") {
warning_(paste0("The input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
"Please update your MO codes with `as.mo()` to increase speed."),
call = FALSE)
warning_("in `mo_", property, "()`: the input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
"Please update your MO codes with `as.mo()` to increase speed.")
} else {
warning_(paste0("The input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
n_solved, " old MO code", ifelse(n_solved == 1, "", "s"),
ifelse(n_solved == 1, " was", " were"),
ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
"to ", ifelse(n_solved == 1, "a ", ""),
"currently used MO code", ifelse(n_solved == 1, "", "s"),
ifelse(n_unsolved > 0,
paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
".")),
call = FALSE)
warning_("in `as.mo()`: the input contained ", n_matched,
" old MO code", ifelse(n_matched == 1, "", "s"),
" (", n_unique, "from a previous AMR package version). ",
n_solved, " old MO code", ifelse(n_solved == 1, "", "s"),
ifelse(n_solved == 1, " was", " were"),
ifelse(all_direct_matches, " updated ", font_bold(" guessed ")),
"to ", ifelse(n_solved == 1, "a ", ""),
"currently used MO code", ifelse(n_solved == 1, "", "s"),
ifelse(n_unsolved > 0,
paste0(" and ", n_unsolved, " old MO code", ifelse(n_unsolved == 1, "", "s"), " could not be updated."),
"."))
}
}
x

2
R/mo_property.R
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@ -684,7 +684,7 @@ mo_url <- function(x, open = FALSE, language = get_AMR_locale(), ...) {
if (isTRUE(open)) {
if (length(u) > 1) {
warning_("Only the first URL will be opened, as `browseURL()` only suports one string.")
warning_("in `mo_url()`: only the first URL will be opened, as `browseURL()` only suports one string.")
}
utils::browseURL(u[1L])
}

2
R/pca.R
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@ -98,7 +98,7 @@ pca <- function(x,
x <- as.data.frame(new_list, stringsAsFactors = FALSE)
if (any(vapply(FUN.VALUE = logical(1), x, function(y) !is.numeric(y)))) {
warning_("Be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with [numeric] variables only. See Examples in ?pca.", call = FALSE)
warning_("in `pca()`: be sure to first calculate the resistance (or susceptibility) of variables with antimicrobial test results, since PCA works with numeric variables only. See Examples in ?pca.", call = FALSE)
}
# set column names

4
R/random.R
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@ -106,7 +106,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
if (nrow(df_new) > 0) {
df <- df_new
} else {
warning_("No rows found that match mo '", mo, "', ignoring argument `mo`", call = FALSE)
warning_("in `random_", tolower(type), "()`: no rows found that match mo '", mo, "', ignoring argument `mo`")
}
}
@ -117,7 +117,7 @@ random_exec <- function(type, size, mo = NULL, ab = NULL) {
if (nrow(df_new) > 0) {
df <- df_new
} else {
warning_("No rows found that match ab '", ab, "', ignoring argument `ab`", call = FALSE)
warning_("in `random_", tolower(type), "()`: no rows found that match ab '", ab, "', ignoring argument `ab`")
}
}

2
R/resistance_predict.R
View File

@ -153,7 +153,7 @@ resistance_predict <- function(x,
x <- dots[which(dots.names == "tbl")]
}
if ("I_as_R" %in% dots.names) {
warning_("`I_as_R is deprecated - use I_as_S instead.", call = FALSE)
warning_("in `resistance_predict()`: I_as_R is deprecated - use I_as_S instead.")
}
}

361
R/rsi.R
View File

@ -233,9 +233,9 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
} else if (!any(c("R", "S", "I") %in% x, na.rm = TRUE) & !all(is.na(x))) {
return(FALSE)
} else {
x <- x[!is.na(x) & !is.null(x) & x != ""]
x <- x[!is.na(x) & !is.null(x) & !x %in% c("", "-", "NULL")]
if (length(x) == 0) {
# no other values than NA or ""
# no other values than empty
cur_col <- get_current_column()
if (!is.null(cur_col)) {
ab <- suppressWarnings(as.ab(cur_col, fast_mode = TRUE, info = FALSE))
@ -257,7 +257,7 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
}
#' @export
# extra param: warn (never throw warning)
# extra param: warn (logical, to never throw a warning)
as.rsi.default <- function(x, ...) {
if (is.rsi(x)) {
return(x)
@ -278,22 +278,23 @@ as.rsi.default <- function(x, ...) {
x[x.bak == 2] <- "I"
x[x.bak == 3] <- "R"
}
} else if (!all(is.na(x)) && !identical(levels(x), c("R", "S", "I")) && !all(x %in% c("R", "S", "I", NA))) {
if (all(x %unlike% "(R|S|I)", na.rm = TRUE)) {
# check if they are actually MICs or disks
if (all_valid_mics(x)) {
warning_("The input seems to contain MIC values. You can transform them with `as.mic()` before running `as.rsi()` to interpret them.", call = FALSE)
warning_("in `as.rsi()`: the input seems to contain MIC values. You can transform them with `as.mic()` before running `as.rsi()` to interpret them.")
} else if (all_valid_disks(x)) {
warning_("The input seems to contain disk diffusion values. You can transform them with `as.disk()` before running `as.rsi()` to interpret them.", call = FALSE)
warning_("in `as.rsi()`: the input seems to contain disk diffusion values. You can transform them with `as.disk()` before running `as.rsi()` to interpret them.")
}
}
# trim leading and trailing spaces, new lines, etc.
x <- trimws2(as.character(unlist(x)))
x[x %in% c(NA, "", "-", "NULL")] <- NA_character_
x.bak <- x
na_before <- length(x[is.na(x) | x == ""])
na_before <- length(x[is.na(x)])
# correct for translations
trans_R <- unlist(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
@ -332,19 +333,19 @@ as.rsi.default <- function(x, ...) {
unique() %pm>%
sort() %pm>%
vector_and(quotes = TRUE)
warning_(na_after - na_before, " results truncated (",
warning_("in `as.rsi()`: ", na_after - na_before, " results truncated (",
round(((na_after - na_before) / length(x)) * 100),
"%) that were invalid antimicrobial interpretations: ",
list_missing, call = FALSE)
}
if (any(toupper(x.bak) == "U") && message_not_thrown_before("as.rsi", "U")) {
warning_("in as.rsi(): 'U' was interpreted as 'S', following some laboratory systems", call = FALSE)
if (any(toupper(x.bak[!is.na(x.bak)]) == "U") && message_not_thrown_before("as.rsi", "U")) {
warning_("in `as.rsi()`: 'U' was interpreted as 'S', following some laboratory systems")
}
if (any(toupper(x.bak) == "D") && message_not_thrown_before("as.rsi", "D")) {
warning_("in as.rsi(): 'D' (dose-dependent) was interpreted as 'I', following some laboratory systems", call = FALSE)
if (any(toupper(x.bak[!is.na(x.bak)]) == "D") && message_not_thrown_before("as.rsi", "D")) {
warning_("in `as.rsi()`: 'D' (dose-dependent) was interpreted as 'I', following some laboratory systems")
}
if (any(toupper(x.bak) == "H") && message_not_thrown_before("as.rsi", "H")) {
warning_("in as.rsi(): 'H' was interpreted as 'I', following some laboratory systems", call = FALSE)
if (any(toupper(x.bak[!is.na(x.bak)]) == "H") && message_not_thrown_before("as.rsi", "H")) {
warning_("in `as.rsi()`: 'H' was interpreted as 'I', following some laboratory systems")
}
}
}
@ -364,89 +365,17 @@ as.rsi.mic <- function(x,
add_intrinsic_resistance = FALSE,
reference_data = AMR::rsi_translation,
...) {
meet_criteria(x)
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"))
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(uti, allow_class = "logical", has_length = c(1, length(x)))
meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
meet_criteria(reference_data, allow_class = "data.frame")
check_reference_data(reference_data)
# for dplyr's across()
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
# try to get current column, which will only be available when in across()
ab <- tryCatch(cur_column_dplyr(),
error = function(e) ab)
}
# for auto-determining mo
mo_var_found <- ""
if (is.null(mo)) {
tryCatch({
df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
mo <- NULL
try({
mo <- suppressMessages(search_type_in_df(df, "mo"))
}, silent = TRUE)
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
mo <- df[, mo, drop = TRUE]
}
}, error = function(e)
stop_('No information was supplied about the microorganisms (missing argument `mo`). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use `data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n",
"To tranform all disk diffusion zones in a data set, use `data %>% as.rsi()` or data %>% mutate_if(is.disk, as.rsi).", call = FALSE)
)
}
if (length(ab) == 1 && ab %like% "as.mic") {
stop_('No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.rsi.', call = FALSE)
}
ab_coerced <- suppressWarnings(as.ab(ab))
mo_coerced <- suppressWarnings(as.mo(mo))
guideline_coerced <- get_guideline(guideline, reference_data)
if (is.na(ab_coerced)) {
message_("Returning NAs for unknown drug: '", font_bold(ab),
"'. Rename this column to a drug name or code, and check the output with `as.ab()`.",
add_fn = font_red,
as_note = FALSE)
return(as.rsi(rep(NA, length(x))))
}
if (length(mo_coerced) == 1) {
mo_coerced <- rep(mo_coerced, length(x))
}
if (length(uti) == 1) {
uti <- rep(uti, length(x))
}
agent_formatted <- paste0("'", font_bold(ab), "'")
agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
}
message_("=> Interpreting MIC values of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
agent_formatted,
mo_var_found,
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
font_bold(guideline_coerced),
"manually defined 'reference_data'"),
"... ",
appendLF = FALSE,
as_note = FALSE)
result <- exec_as.rsi(method = "mic",
x = x,
mo = mo_coerced,
ab = ab_coerced,
guideline = guideline_coerced,
uti = uti,
conserve_capped_values = conserve_capped_values,
add_intrinsic_resistance = add_intrinsic_resistance,
reference_data = reference_data) # exec_as.rsi will return message 'OK'
result
as_rsi_method(method_short = "mic",
method_long = "MIC values",
x = x,
mo = mo,
ab = ab,
guideline = guideline,
uti = uti,
conserve_capped_values = conserve_capped_values,
add_intrinsic_resistance = add_intrinsic_resistance,
reference_data = reference_data,
...)
}
#' @rdname as.rsi
@ -459,88 +388,17 @@ as.rsi.disk <- function(x,
add_intrinsic_resistance = FALSE,
reference_data = AMR::rsi_translation,
...) {
meet_criteria(x)
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"))
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(uti, allow_class = "logical", has_length = c(1, length(x)))
meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
meet_criteria(reference_data, allow_class = "data.frame")
check_reference_data(reference_data)
# for dplyr's across()
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
# try to get current column, which will only be available when in across()
ab <- tryCatch(cur_column_dplyr(),
error = function(e) ab)
}
# for auto-determining mo
mo_var_found <- ""
if (is.null(mo)) {
tryCatch({
df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
mo <- NULL
try({
mo <- suppressMessages(search_type_in_df(df, "mo"))
}, silent = TRUE)
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
mo <- df[, mo, drop = TRUE]
}
}, error = function(e)
stop_('No information was supplied about the microorganisms (missing argument `mo`). See ?as.rsi.\n\n',
"To transform certain columns with e.g. mutate_at(), use `data %>% mutate_at(vars(...), as.rsi, mo = .$x)`, where x is your column with microorganisms.\n",
"To tranform all disk diffusion zones in a data set, use `data %>% as.rsi()` or data %>% mutate_if(is.disk, as.rsi).", call = FALSE)
)
}
if (length(ab) == 1 && ab %like% "as.disk") {
stop_('No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.rsi.', call = FALSE)
}
ab_coerced <- suppressWarnings(as.ab(ab))
mo_coerced <- suppressWarnings(as.mo(mo))
guideline_coerced <- get_guideline(guideline, reference_data)
if (is.na(ab_coerced)) {
message_("Returning NAs for unknown drug: '", font_bold(ab),
"'. Rename this column to a drug name or code, and check the output with `as.ab()`.",
add_fn = font_red,
as_note = FALSE)
return(as.rsi(rep(NA, length(x))))
}
if (length(mo_coerced) == 1) {
mo_coerced <- rep(mo_coerced, length(x))
}
if (length(uti) == 1) {
uti <- rep(uti, length(x))
}
agent_formatted <- paste0("'", font_bold(ab), "'")
agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
}
message_("=> Interpreting disk zones of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
agent_formatted,
mo_var_found,
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
font_bold(guideline_coerced),
"manually defined 'reference_data'"),
"... ",
appendLF = FALSE,
as_note = FALSE)
result <- exec_as.rsi(method = "disk",
x = x,
mo = mo_coerced,
ab = ab_coerced,
guideline = guideline_coerced,
uti = uti,
conserve_capped_values = FALSE,
add_intrinsic_resistance = add_intrinsic_resistance,
reference_data = reference_data) # exec_as.rsi will return message 'OK'
result
as_rsi_method(method_short = "disk",
method_long = "disk diffusion zones",
x = x,
mo = mo,
ab = ab,
guideline = guideline,
uti = uti,
conserve_capped_values = FALSE,
add_intrinsic_resistance = add_intrinsic_resistance,
reference_data = reference_data,
...)
}
#' @rdname as.rsi
@ -560,7 +418,7 @@ as.rsi.data.frame <- function(x,
meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
meet_criteria(reference_data, allow_class = "data.frame")
x.bak <- x
for (i in seq_len(ncol(x))) {
# don't keep factors, overwriting them is hard
@ -574,7 +432,7 @@ as.rsi.data.frame <- function(x,
if (is.null(col_mo)) {
col_mo <- search_type_in_df(x = x, type = "mo", info = FALSE)
}
# -- UTIs
col_uti <- uti
if (is.null(col_uti)) {
@ -615,7 +473,7 @@ as.rsi.data.frame <- function(x,
uti <- FALSE
}
}
i <- 0
if (tryCatch(length(list(...)) > 0, error = function(e) TRUE)) {
sel <- colnames(pm_select(x, ...))
@ -625,7 +483,7 @@ as.rsi.data.frame <- function(x,
if (!is.null(col_mo)) {
sel <- sel[sel != col_mo]
}
ab_cols <- colnames(x)[vapply(FUN.VALUE = logical(1), x, function(y) {
i <<- i + 1
check <- is.mic(y) | is.disk(y)
@ -648,7 +506,7 @@ as.rsi.data.frame <- function(x,
return(FALSE)
}
})]
stop_if(length(ab_cols) == 0,
"no columns with MIC values, disk zones or antibiotic column names found in this data set. Use as.mic() or as.disk() to transform antimicrobial columns.")
# set type per column
@ -667,7 +525,7 @@ as.rsi.data.frame <- function(x,
}
x_mo <- as.mo(x[, col_mo, drop = TRUE])
}
for (i in seq_len(length(ab_cols))) {
if (types[i] == "mic") {
x[, ab_cols[i]] <- as.rsi(x = x %pm>%
@ -745,6 +603,106 @@ get_guideline <- function(guideline, reference_data) {
guideline_param
}
as_rsi_method <- function(method_short = "mic",
method_long = "MIC values",
x = x,
mo = NULL,
ab = deparse(substitute(x)),
guideline = "EUCAST",
uti = FALSE,
conserve_capped_values = FALSE,
add_intrinsic_resistance = FALSE,
reference_data = AMR::rsi_translation,
...) {
meet_criteria(x)
meet_criteria(mo, allow_class = c("mo", "character"), allow_NULL = TRUE)
meet_criteria(ab, allow_class = c("ab", "character"))
meet_criteria(guideline, allow_class = "character", has_length = 1)
meet_criteria(uti, allow_class = "logical", has_length = c(1, length(x)))
meet_criteria(conserve_capped_values, allow_class = "logical", has_length = 1)
meet_criteria(add_intrinsic_resistance, allow_class = "logical", has_length = 1)
meet_criteria(reference_data, allow_class = "data.frame")
check_reference_data(reference_data)
# for dplyr's across()
cur_column_dplyr <- import_fn("cur_column", "dplyr", error_on_fail = FALSE)
if (!is.null(cur_column_dplyr) && tryCatch(is.data.frame(get_current_data("ab", call = 0)), error = function(e) FALSE)) {
# try to get current column, which will only be available when in across()
ab <- tryCatch(cur_column_dplyr(),
error = function(e) ab)
}
# for auto-determining mo
mo_var_found <- ""
if (is.null(mo)) {
tryCatch({
df <- get_current_data(arg_name = "mo", call = -3) # will return an error if not found
mo <- NULL
try({
mo <- suppressMessages(search_type_in_df(df, "mo"))
}, silent = TRUE)
if (!is.null(df) && !is.null(mo) && is.data.frame(df)) {
mo_var_found <- paste0(" based on column '", font_bold(mo), "'")
mo <- df[, mo, drop = TRUE]
}
}, error = function(e) {
mo <- NULL
})
}
if (is.null(mo)) {
stop_("No information was supplied about the microorganisms (missing argument `mo` and no column of class <mo> found). See ?as.rsi.\n\n",
"To transform certain columns with e.g. mutate(), use `data %>% mutate(across(..., as.rsi, mo = x))`, where x is your column with microorganisms.\n",
"To tranform all ", method_long, " in a data set, use `data %>% as.rsi()` or `data %>% mutate(across(where(is.", method_short, "), as.rsi))`.", call = FALSE)
}
if (length(ab) == 1 && ab %like% paste0("as.", method_short)) {
stop_('No unambiguous name was supplied about the antibiotic (argument `ab`). See ?as.rsi.', call = FALSE)
}
ab_coerced <- suppressWarnings(as.ab(ab))
mo_coerced <- suppressWarnings(as.mo(mo))
guideline_coerced <- get_guideline(guideline, reference_data)
if (is.na(ab_coerced)) {
message_("Returning NAs for unknown drug: '", font_bold(ab),
"'. Rename this column to a drug name or code, and check the output with `as.ab()`.",
add_fn = font_red,
as_note = FALSE)
return(as.rsi(rep(NA, length(x))))
}
if (length(mo_coerced) == 1) {
mo_coerced <- rep(mo_coerced, length(x))
}
if (length(uti) == 1) {
uti <- rep(uti, length(x))
}
agent_formatted <- paste0("'", font_bold(ab), "'")
agent_name <- ab_name(ab_coerced, tolower = TRUE, language = NULL)
if (generalise_antibiotic_name(ab) != generalise_antibiotic_name(agent_name)) {
agent_formatted <- paste0(agent_formatted, " (", ab_coerced, ", ", agent_name, ")")
}
message_("=> Interpreting ", method_long, " of ", ifelse(isTRUE(list(...)$is_data.frame), "column ", ""),
agent_formatted,
mo_var_found,
" according to ", ifelse(identical(reference_data, AMR::rsi_translation),
font_bold(guideline_coerced),
"manually defined 'reference_data'"),
"... ",
appendLF = FALSE,
as_note = FALSE)
result <- exec_as.rsi(method = method_short,
x = x,
mo = mo_coerced,
ab = ab_coerced,
guideline = guideline_coerced,
uti = uti,
conserve_capped_values = conserve_capped_values,
add_intrinsic_resistance = add_intrinsic_resistance,
reference_data = reference_data) # exec_as.rsi will return message 'OK'
result
}
exec_as.rsi <- function(method,
x,
mo,
@ -767,7 +725,7 @@ exec_as.rsi <- function(method,
x <- as.disk(x) # when as.rsi.disk is called directly
}
warned <- FALSE
rise_warning <- FALSE
method_param <- toupper(method)
genera <- mo_genus(mo, language = NULL)
@ -812,13 +770,6 @@ exec_as.rsi <- function(method,
lookup_lancefield <- paste(mo_lancefield, ab)
lookup_other <- paste(mo_other, ab)
if (length(unique(paste(trans$mo, trans$ab))) == length(unique(paste(trans$mo, trans$ab, trans$uti))) &&
any(trans$uti == TRUE, na.rm = TRUE) && all(uti == FALSE)) {
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
warning_("Introducing NA: interpretation of ", font_bold(ab_name(ab, tolower = TRUE)), " for some microorganisms is only available for (uncomplicated) urinary tract infections (UTI). Use argument `uti` to set which isolates are from urine. See ?as.rsi.", call = FALSE)
warned <- TRUE
}
any_is_intrinsic_resistant <- FALSE
for (i in seq_len(length(x))) {
@ -828,7 +779,7 @@ exec_as.rsi <- function(method,
if (isTRUE(add_intrinsic_resistance) & is_intrinsic_r) {
if (guideline_coerced %unlike% "EUCAST") {
if (message_not_thrown_before("as.rsi", "msg2")) {
warning_("Using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.", call = FALSE)
warning_("in `as.rsi()`: using 'add_intrinsic_resistance' is only useful when using EUCAST guidelines, since the rules for intrinsic resistance are based on EUCAST.")
}
} else {
new_rsi[i] <- "R"
@ -837,7 +788,7 @@ exec_as.rsi <- function(method,
}
get_record <- trans %pm>%
# no subsetting to UTI for now
# no subsetting to UTI here
subset(lookup %in% c(lookup_mo[i],
lookup_genus[i],
lookup_family[i],
@ -846,6 +797,11 @@ exec_as.rsi <- function(method,
lookup_lancefield[i],
lookup_other[i]))
if (any(get_record$uti == TRUE, na.rm = TRUE) && message_not_thrown_before("as.rsi", "msg3", ab)) {
warning_("in `as.rsi()`: interpretation of ", font_bold(ab_name(ab, tolower = TRUE)), " is only available for (uncomplicated) urinary tract infections (UTI) for some microorganisms. Use argument `uti` to set which isolates are from urine. See ?as.rsi.")
rise_warning <- TRUE
}
if (isTRUE(uti[i])) {
get_record <- get_record %pm>%
# be as specific as possible (i.e. prefer species over genus):
@ -856,7 +812,7 @@ exec_as.rsi <- function(method,
pm_filter(uti == FALSE) %pm>% # 'uti' is a column in rsi_translation
pm_arrange(rank_index)
}
get_record <- get_record[1L, , drop = FALSE]
if (NROW(get_record) > 0) {
@ -885,11 +841,10 @@ exec_as.rsi <- function(method,
if (any_is_intrinsic_resistant & guideline_coerced %like% "EUCAST" & !isTRUE(add_intrinsic_resistance)) {
# found some intrinsic resistance, but was not applied
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
if (message_not_thrown_before("as.rsi", "msg3")) {
warning_("Found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.", call = FALSE)
if (message_not_thrown_before("as.rsi", "msg4")) {
warning_("in `as.rsi()`: found intrinsic resistance in some bug/drug combinations, although it was not applied.\nUse `as.rsi(..., add_intrinsic_resistance = TRUE)` to apply it.")
}
warned <- TRUE
rise_warning <- TRUE
}
new_rsi <- x_bak %pm>%
@ -898,7 +853,9 @@ exec_as.rsi <- function(method,
by = "x_mo") %pm>%
pm_pull(new_rsi)
if (warned == FALSE) {
if (isTRUE(rise_warning)) {
message_("WARNING.", add_fn = list(font_yellow, font_bold), as_note = FALSE)
} else {
message_(" OK.", add_fn = list(font_green, font_bold), as_note = FALSE)
}

2
R/rsi_calc.R
View File

@ -95,7 +95,7 @@ rsi_calc <- function(...,
}
if (is.null(x)) {
warning_("argument is NULL (check if columns exist): returning NA", call = FALSE)
warning_("argument is NULL (check if columns exist): returning NA")
if (as_percent == TRUE) {
return(NA_character_)
} else {

2
R/translate.R
View File

@ -193,7 +193,7 @@ translate_AMR <- function(from,
any_form_in_patterns <- tryCatch(
any(from_unique %like% paste0("(", paste(gsub(" +\\(.*", "", df_trans$pattern), collapse = "|"), ")")),
error = function(e) {
warning_("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).", call = FALSE)
warning_("Translation not possible. Please open an issue on GitHub (https://github.com/msberends/AMR/issues).")
return(FALSE)
})

BIN
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4
docs/404.html
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@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span>
</div>
@ -210,7 +210,7 @@ Content not found. Please use links in the navbar.
<div class="pkgdown">
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer>

4
docs/LICENSE-text.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span>
</div>
@ -420,7 +420,7 @@ END OF TERMS AND CONDITIONS
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

4
docs/articles/datasets.html
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@ -44,7 +44,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span>
</div>
@ -190,7 +190,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">26 February 2022</h4>
<h4 data-toc-skip class="date">02 March 2022</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>

6
docs/authors.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span>
</div>
@ -218,7 +218,7 @@
</p>
</li>
<li>
<p><strong>Anthony Underwood</strong>. Contributor. <a href="https://orcid.org/0000-0002-8547-427" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
<p><strong>Anthony Underwood</strong>. Contributor. <a href="https://orcid.org/0000-0002-8547-4277" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
</p>
</li>
</ul></div>
@ -273,7 +273,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

8
docs/index.html
View File

@ -47,7 +47,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span>
</div>
@ -214,7 +214,7 @@
</h5>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span class="co"># AMR works great with dplyr, but it's not required or neccesary</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span>
<span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span>
<span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span>
@ -340,7 +340,7 @@
</h4>
<p>The development of this package is part of, related to, or made possible by:</p>
<div align="center">
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="http://www.eurhealth-1health.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
<p><a href="https://www.rug.nl" title="University of Groningen" class="external-link"><img src="./logo_rug.png" class="partner_logo"></a> <a href="https://www.umcg.nl" title="University Medical Center Groningen" class="external-link"><img src="./logo_umcg.png" class="partner_logo"></a> <a href="https://www.certe.nl" title="Certe Medical Diagnostics and Advice Foundation" class="external-link"><img src="./logo_certe.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="EurHealth-1-Health" class="external-link"><img src="./logo_eh1h.png" class="partner_logo"></a> <a href="https://www.deutschland-nederland.eu" title="INTERREG" class="external-link"><img src="./logo_interreg.png" class="partner_logo"></a></p>
</div>
</div>
</div>
@ -561,7 +561,7 @@
<div class="pkgdown">
<p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer>

13
docs/news/index.html
View File

@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span>
</div>
@ -157,13 +157,13 @@
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.8.0.9001" id="amr-1809001">
<code>AMR</code> 1.8.0.9001<a class="anchor" aria-label="anchor" href="#amr-1809001"></a></h2>
<h2 class="page-header" data-toc-text="1.8.0.9002" id="amr-1809002">
<code>AMR</code> 1.8.0.9002<a class="anchor" aria-label="anchor" href="#amr-1809002"></a></h2>
<div class="section level3">
<h3 id="last-updated-february-1-8-0-9001"><small>Last updated: 26 February 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-february-1-8-0-9001"></a></h3>
<h3 id="last-updated-march-1-8-0-9002"><small>Last updated: 2 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9002"></a></h3>
<p>All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p>
<div class="section level4">
<h4 id="changed-1-8-0-9001">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9001"></a></h4>
<h4 id="changed-1-8-0-9002">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9002"></a></h4>
<ul><li><p>Support for antibiotic interpretations of the MIPS laboratory system: <code>"U"</code> for S (‘susceptible urine’), <code>"D"</code> for I (‘susceptible dose-dependent’)</p></li>
<li>
<p>Improved algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code>, especially for ignoring non-taxonomic text, such as:</p>
@ -172,9 +172,10 @@
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"methicillin-resistant S. aureus (MRSA)"</span><span class="op">)</span>
<span class="co">#&gt; [1] "Staphylococcus aureus"</span></code></pre></div>
</li>
<li><p>More informative warning messages</p></li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-0-9001">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9001"></a></h4>
<h4 id="other-1-8-0-9002">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9002"></a></h4>
<ul><li>Fix for unit testing on R 3.3</li>
<li>Fix for size of some image elements, as requested by CRAN</li>
</ul></div>

4
docs/survey.html
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@ -17,7 +17,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span>
</div>
@ -172,7 +172,7 @@
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.0.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
</div>
</footer></div>

6
git_development.sh
View File

@ -142,14 +142,12 @@ if [ $lazy == "FALSE" ]; then
Rscript -e "devtools::install(quiet = TRUE, dependencies = FALSE)"
Rscript -e "suppressMessages(pkgdown::build_site(lazy = FALSE, examples = FALSE, install = FALSE))"
else
# always build home page
Rscript -e "pkgdown::build_home()"
if ! git diff --quiet man; then
# documentation has changed
Rscript -e "pkgdown::build_reference(lazy = $lazy, examples = FALSE)"
fi
if ! git diff --quiet index.md; then
# home page has changed
Rscript -e "pkgdown::build_home()"
fi
if ! git diff --quiet NEWS.md; then
# news has changed
Rscript -e "pkgdown::build_news()"

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(