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(v2.1.1.9052) unit test fix

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dr. M.S. (Matthijs) Berends 2024-06-16 20:53:50 +02:00
parent 4ffac7e22d
commit 68f7795481
7 changed files with 106 additions and 61 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 2.1.1.9051
Version: 2.1.1.9052
Date: 2024-06-16
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

1
NAMESPACE
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@ -96,6 +96,7 @@ S3method(print,mo_renamed)
S3method(print,mo_uncertainties)
S3method(print,pca)
S3method(print,sir)
S3method(print,sir_log)
S3method(quantile,mic)
S3method(rep,ab)
S3method(rep,av)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 2.1.1.9051
# AMR 2.1.1.9052
*(this beta version will eventually become v3.0. We're happy to reach a new major milestone soon, which will be all about the new One Health support!)*

4
R/ab_selectors.R
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@ -63,7 +63,7 @@
#' # dplyr -------------------------------------------------------------------
#'
#' if (require("dplyr")) {
#'. example_isolates %>% select(carbapenems())
#' example_isolates %>% select(carbapenems())
#' }
#'
#' if (require("dplyr")) {
@ -73,7 +73,7 @@
#'
#' if (require("dplyr")) {
#' # select only antibiotic columns with DDDs for oral treatment
#'. example_isolates %>% select(administrable_per_os())
#' example_isolates %>% select(administrable_per_os())
#' }
#'
#' if (require("dplyr")) {

150
R/sir.R
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@ -1002,14 +1002,13 @@ as_sir_method <- function(method_short,
""),
"... ")
msg_note <- function(messages) {
msg_note <- function(messages, font_fn = font_black) {
messages <- unique(messages)
for (i in seq_len(length(messages))) {
messages[i] <- word_wrap(extra_indent = 5, messages[i])
}
message(
font_yellow_bg(paste0(" NOTE", ifelse(length(messages) > 1, "S", ""), " \n")),
paste0(" ", font_black(AMR_env$bullet_icon), " ", font_black(messages, collapse = NULL), collapse = "\n")
paste0(" ", font_fn(AMR_env$bullet_icon), " ", font_fn(messages, collapse = NULL), collapse = "\n")
)
}
@ -1018,7 +1017,7 @@ as_sir_method <- function(method_short,
metadata_mo <- get_mo_uncertainties()
rise_warning <- FALSE
rise_note <- FALSE
rise_notes <- FALSE
method_coerced <- toupper(method)
ab_coerced <- as.ab(ab)
@ -1070,7 +1069,7 @@ as_sir_method <- function(method_short,
subset(mo != "UNKNOWN" & ref_tbl %unlike% "PK.*PD")
}
msgs <- character(0)
notes <- character(0)
if (guideline_coerced %like% "EUCAST") {
any_is_intrinsic_resistant <- FALSE
@ -1097,6 +1096,14 @@ as_sir_method <- function(method_short,
return(rep(NA_sir_, nrow(df)))
}
vectorise_log_entry <- function(x, len) {
if (length(x) == 1 && len > 1) {
rep(x, len)
} else {
x
}
}
# run the rules (df_unique is a row combination per mo/ab/uti/host)
for (i in seq_len(nrow(df_unique))) {
p$tick()
@ -1136,7 +1143,6 @@ as_sir_method <- function(method_short,
suppressMessages(suppressWarnings(ab_name(ab_current, language = NULL, tolower = TRUE))),
" (", ab_current, ")"
)
notes <- character(0)
# gather all available breakpoints for current MO
breakpoints_current <- breakpoints %pm>%
@ -1147,6 +1153,34 @@ as_sir_method <- function(method_short,
mo_current_species_group,
mo_current_other
))
if (NROW(breakpoints_current) == 0) {
# no note about missing breakpoints - it's already in the header before the interpretation starts
AMR_env$sir_interpretation_history <- rbind_AMR(
AMR_env$sir_interpretation_history,
# recycling 1 to 2 rows does not always seem to work, which is why vectorise_log_entry() was added
data.frame(
datetime = vectorise_log_entry(Sys.time(), length(rows)),
index = rows,
ab_user = vectorise_log_entry(ab.bak[match(ab_current, df$ab)][1], length(rows)),
mo_user = vectorise_log_entry(mo.bak[match(mo_current, df$mo)][1], length(rows)),
ab = vectorise_log_entry(ab_current, length(rows)),
mo = vectorise_log_entry(mo_current, length(rows)),
method = vectorise_log_entry(method_coerced, length(rows)),
input = vectorise_log_entry(as.double(values), length(rows)),
outcome = vectorise_log_entry(NA_sir_, length(rows)),
host = vectorise_log_entry(host_current, length(rows)),
notes = vectorise_log_entry("NO BREAKPOINT AVAILABLE", length(rows)),
guideline = vectorise_log_entry(guideline_coerced, length(rows)),
ref_table = vectorise_log_entry(NA_character_, length(rows)),
uti = vectorise_log_entry(uti_current, length(rows)),
breakpoint_S_R = vectorise_log_entry(NA_character_, length(rows)),
stringsAsFactors = FALSE
)
)
next
}
# set the host index according to most available breakpoints (see R/zzz.R where this is set in the pkg environment)
breakpoints_current$host_index <- match(breakpoints_current$host, c("human", "ECOFF", AMR_env$host_preferred_order))
@ -1154,6 +1188,7 @@ as_sir_method <- function(method_short,
# (this will e.g. prefer 'species' breakpoints over 'order' breakpoints)
if (all(uti_current == FALSE, na.rm = TRUE)) {
breakpoints_current <- breakpoints_current %pm>%
# `uti` is a column in the data set
# this will put UTI = FALSE first, then UTI = NA, then UTI = TRUE
pm_mutate(uti_index = ifelse(is.na(uti) & uti == FALSE, 1,
ifelse(is.na(uti), 2,
@ -1167,11 +1202,6 @@ as_sir_method <- function(method_short,
pm_arrange(host_index, rank_index)
}
if (NROW(breakpoints_current) == 0) {
# no note about missing breakpoints - it's already in the header before the interpretation starts
next
}
# veterinary host check
host_current <- unique(df_unique[i, "host", drop = TRUE])[1]
breakpoints_current$host_match <- breakpoints_current$host == host_current
@ -1181,12 +1211,12 @@ as_sir_method <- function(method_short,
subset(host_match == TRUE)
} else {
# no breakpoint found for this host, so sort on mostly available guidelines
notes <- c(notes, paste0("No breakpoints available for ", font_bold(host_current), " for ", ab_formatted, " in ", mo_formatted, " - using ", font_bold(breakpoints_current$host[1]), " instead."))
# msgs <- c(msgs, paste0("No breakpoints available for ", font_bold(host_current), " for ", ab_formatted, " in ", mo_formatted, " - using ", font_bold(breakpoints_current$host[1]), " instead."))
notes <- c(notes, paste0("Using ", font_bold(breakpoints_current$host[1]), " breakpoints since ", font_bold(host_current), " for ", ab_formatted, " in ", mo_formatted, " are not available."))
rise_notes <- TRUE
}
}
# throw notes for different body sites
# throw messages for different body sites
site <- breakpoints_current[1L, "site", drop = FALSE] # this is the one we'll take
if (is.na(site)) {
site <- paste0("an unspecified body site")
@ -1195,21 +1225,20 @@ as_sir_method <- function(method_short,
}
if (nrow(breakpoints_current) == 1 && all(breakpoints_current$uti == TRUE) && any(uti_current %in% c(FALSE, NA)) && message_not_thrown_before("as.sir", "uti", ab_current)) {
# only UTI breakpoints available
warning_("in `as.sir()`: interpretation of ", font_bold(ab_formatted), " is only available for (uncomplicated) urinary tract infections (UTI) for some microorganisms, thus assuming `uti = TRUE`. See `?as.sir`.")
rise_warning <- TRUE
notes <- c(notes, paste0("Breakpoints for ", font_bold(ab_formatted), " in ", mo_formatted, " are only available for (uncomplicated) urinary tract infections (UTI); assuming `uti = TRUE`."))
} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && any(is.na(uti_current)) && all(c(TRUE, FALSE) %in% breakpoints_current$uti, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteUTI", mo_current, ab_current)) {
# both UTI and Non-UTI breakpoints available
msgs <- c(msgs, paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`."))
notes <- c(notes, paste0("Breakpoints for UTI ", font_bold("and"), " non-UTI available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, ". Use argument `uti` to set which isolates are from urine. See `?as.sir`."))
breakpoints_current <- breakpoints_current %pm>%
pm_filter(uti == FALSE)
} else if (nrow(breakpoints_current) > 1 && length(unique(breakpoints_current$site)) > 1 && all(breakpoints_current$uti == FALSE, na.rm = TRUE) && message_not_thrown_before("as.sir", "siteOther", mo_current, ab_current)) {
# breakpoints for multiple body sites available
msgs <- c(msgs, paste0("Multiple breakpoints available for ", ab_formatted, " in ", mo_formatted, " - assuming ", site, "."))
notes <- c(notes, paste0("Multiple breakpoints available for ", font_bold(ab_formatted), " in ", mo_formatted, " - assuming ", site, "."))
}
# first check if mo is intrinsic resistant
if (isTRUE(add_intrinsic_resistance) && guideline_coerced %like% "EUCAST" && paste(mo_current, ab_current) %in% AMR_env$intrinsic_resistant) {
msgs <- c(msgs, paste0("Intrinsic resistance applied for ", ab_formatted, " in ", mo_formatted, ""))
notes <- c(notes, paste0("Intrinsic resistance applied for ", ab_formatted, " in ", mo_formatted, ""))
new_sir <- rep(as.sir("R"), length(rows))
} else if (nrow(breakpoints_current) == 0) {
# no rules available
@ -1219,10 +1248,10 @@ as_sir_method <- function(method_short,
breakpoints_current <- breakpoints_current[1L, , drop = FALSE]
if (any(breakpoints_current$mo == "UNKNOWN", na.rm = TRUE) | any(breakpoints_current$ref_tbl %like% "PK.*PD", na.rm = TRUE)) {
msgs <- c(msgs, "Some PK/PD breakpoints were applied - use `include_PKPD = FALSE` to prevent this")
notes <- c(notes, "Some PK/PD breakpoints were applied - use `include_PKPD = FALSE` to prevent this")
}
if (any(breakpoints_current$site %like% "screen", na.rm = TRUE) | any(breakpoints_current$ref_tbl %like% "screen", na.rm = TRUE)) {
msgs <- c(msgs, "Some screening breakpoints were applied - use `include_screening = FALSE` to prevent this")
notes <- c(notes, "Some screening breakpoints were applied - use `include_screening = FALSE` to prevent this")
}
if (method == "mic") {
@ -1252,23 +1281,23 @@ as_sir_method <- function(method_short,
# write to verbose output
AMR_env$sir_interpretation_history <- rbind_AMR(
AMR_env$sir_interpretation_history,
# recycling 1 to 2 rows does not seem to work, which is why rep() was added
# recycling 1 to 2 rows does not always seem to work, which is why vectorise_log_entry() was added
data.frame(
datetime = rep(Sys.time(), length(rows)),
datetime = vectorise_log_entry(Sys.time(), length(rows)),
index = rows,
ab_user = rep(ab.bak[match(ab_current, df$ab)][1], length(rows)),
mo_user = rep(mo.bak[match(mo_current, df$mo)][1], length(rows)),
ab = rep(ab_current, length(rows)),
mo = rep(breakpoints_current[, "mo", drop = TRUE], length(rows)),
method = rep(method_coerced, length(rows)),
input = as.double(values),
outcome = as.sir(new_sir),
host = rep(breakpoints_current[, "host", drop = TRUE], length(rows)),
notes = rep(paste0(notes, collapse = " "), length(rows)),
guideline = rep(guideline_coerced, length(rows)),
ref_table = rep(breakpoints_current[, "ref_tbl", drop = TRUE], length(rows)),
uti = rep(breakpoints_current[, "uti", drop = TRUE], length(rows)),
breakpoint_S_R = rep(paste0(breakpoints_current[, "breakpoint_S", drop = TRUE], "-", breakpoints_current[, "breakpoint_R", drop = TRUE]), length(rows)),
ab_user = vectorise_log_entry(ab.bak[match(ab_current, df$ab)][1], length(rows)),
mo_user = vectorise_log_entry(mo.bak[match(mo_current, df$mo)][1], length(rows)),
ab = vectorise_log_entry(breakpoints_current[, "ab", drop = TRUE], length(rows)),
mo = vectorise_log_entry(breakpoints_current[, "mo", drop = TRUE], length(rows)),
method = vectorise_log_entry(method_coerced, length(rows)),
input = vectorise_log_entry(as.double(values), length(rows)),
outcome = vectorise_log_entry(as.sir(new_sir), length(rows)),
host = vectorise_log_entry(breakpoints_current[, "host", drop = TRUE], length(rows)),
notes = vectorise_log_entry(paste0(font_stripstyle(notes), collapse = "\n"), length(rows)),
guideline = vectorise_log_entry(guideline_coerced, length(rows)),
ref_table = vectorise_log_entry(breakpoints_current[, "ref_tbl", drop = TRUE], length(rows)),
uti = vectorise_log_entry(breakpoints_current[, "uti", drop = TRUE], length(rows)),
breakpoint_S_R = vectorise_log_entry(paste0(breakpoints_current[, "breakpoint_S", drop = TRUE], "-", breakpoints_current[, "breakpoint_R", drop = TRUE]), length(rows)),
stringsAsFactors = FALSE
)
)
@ -1278,7 +1307,7 @@ as_sir_method <- function(method_short,
}
close(p)
# printing messages
if (has_progress_bar == TRUE) {
# the progress bar has overwritten the intro text, so:
@ -1286,16 +1315,20 @@ as_sir_method <- function(method_short,
}
if (isTRUE(rise_warning)) {
message(font_rose_bg(" WARNING "))
} else if (length(notes) > 0) {
message(font_yellow_bg(" NOTES "))
} else if (length(msgs) == 0) {
message(font_green_bg(" OK "))
} else if (isTRUE(rise_notes)) {
message(font_yellow_bg(paste0(" NOTE", ifelse(length(notes) > 1, "S ", " "))))
if (length(notes) > 1) {
plural <- c("were", "s", "them")
} else {
plural <- c("was", "", "it")
}
message(word_wrap(" ", AMR_env$bullet_icon, " There ", plural[1], " ", length(notes), " note", plural[2], ". Print or View `sir_interpretation_history()` to examine ", plural[3], ".", add_fn = font_black))
} else {
msg_note(sort(msgs))
message(font_green_bg(" OK "))
}
load_mo_uncertainties(metadata_mo)
df$result
}
@ -1306,24 +1339,33 @@ sir_interpretation_history <- function(clean = FALSE) {
meet_criteria(clean, allow_class = "logical", has_length = 1)
out <- AMR_env$sir_interpretation_history
if (NROW(out) == 0) {
message_("No results to return. Run `as.sir()` on MIC values or disk diffusion zones first to see a 'logbook' data set here.")
return(invisible(NULL))
}
out$outcome <- as.sir(out$outcome)
if (NROW(out) > 0) {
# sort descending on time
out <- out[order(out$datetime, out$index, decreasing = TRUE), , drop = FALSE]
}
# keep stored for next use
if (isTRUE(clean)) {
AMR_env$sir_interpretation_history <- AMR_env$sir_interpretation_history[0, , drop = FALSE]
}
# sort descending on time
out <- out[order(out$datetime, decreasing = TRUE), , drop = FALSE]
if (pkg_is_available("tibble")) {
import_fn("as_tibble", "tibble")(out)
} else {
out
out <- import_fn("as_tibble", "tibble")(out)
}
structure(out, class = c("sir_log", class(out)))
}
#' @method print sir_log
#' @export
#' @noRd
print.sir_log <- function(x, ...) {
if (NROW(x) == 0) {
message_("No results to print. Run `as.sir()` on MIC values or disk diffusion zones first to print a 'logbook' data set here.")
return(invisible(NULL))
}
class(x) <- class(x)[class(x) != "sir_log"]
print(x, ...)
}
# will be exported using s3_register() in R/zzz.R

4
inst/tinytest/test-custom_microorganisms.R
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@ -28,7 +28,7 @@
# ==================================================================== #
expect_identical(as.mo("Enterobacter asburiae/cloacae"),
as.mo("Enterobacter cloacae cloacae"))
as.mo("Enterobacter asburiae"))
suppressMessages(
add_custom_microorganisms(
@ -44,3 +44,5 @@ expect_identical(mo_gramstain("ENT_ASB_CLO", language = NULL), "Gram-negative")
expect_identical(paste("B", AMR:::abbreviate_mo("Klebsiella"), AMR:::abbreviate_mo("pneumoniae", 4), sep = "_"),
as.character(as.mo("Klebsiella pneumoniae")))
expect_identical(paste("B", AMR:::abbreviate_mo("Aerococcus"), AMR:::abbreviate_mo("urinae", 4), sep = "_"),
as.character(as.mo("Aerococcus urinae")))

4
man/antibiotic_class_selectors.Rd
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@ -191,7 +191,7 @@ example_isolates
# dplyr -------------------------------------------------------------------
if (require("dplyr")) {
. example_isolates \%>\% select(carbapenems())
example_isolates \%>\% select(carbapenems())
}
if (require("dplyr")) {
@ -201,7 +201,7 @@ if (require("dplyr")) {
if (require("dplyr")) {
# select only antibiotic columns with DDDs for oral treatment
. example_isolates \%>\% select(administrable_per_os())
example_isolates \%>\% select(administrable_per_os())
}
if (require("dplyr")) {