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)
}
diff --git a/R/rsi_calc.R b/R/rsi_calc.R
index 4b7a44d5..9e5120c2 100755
--- a/R/rsi_calc.R
+++ b/R/rsi_calc.R
@@ -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 {
diff --git a/R/translate.R b/R/translate.R
index 010ec3d3..d9df85b5 100755
--- a/R/translate.R
+++ b/R/translate.R
@@ -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)
})
diff --git a/data-raw/AMR_latest.tar.gz b/data-raw/AMR_latest.tar.gz
index 33275e8c..fb64b487 100644
Binary files a/data-raw/AMR_latest.tar.gz and b/data-raw/AMR_latest.tar.gz differ
diff --git a/docs/404.html b/docs/404.html
index 13c09a7f..46da8f50 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -43,7 +43,7 @@
AMR (for R)
- 1.8.0
+ 1.8.0.9002
@@ -210,7 +210,7 @@ Content not found. Please use links in the navbar.
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html
index bc650579..5c243f5b 100644
--- a/docs/LICENSE-text.html
+++ b/docs/LICENSE-text.html
@@ -17,7 +17,7 @@
AMR (for R)
- 1.8.0
+ 1.8.0.9002
@@ -420,7 +420,7 @@ END OF TERMS AND CONDITIONS
diff --git a/docs/articles/datasets.html b/docs/articles/datasets.html
index f1dbfe8b..b951d7e2 100644
--- a/docs/articles/datasets.html
+++ b/docs/articles/datasets.html
@@ -44,7 +44,7 @@
AMR (for R)
- 1.8.0.9001
+ 1.8.0.9002
@@ -190,7 +190,7 @@
@@ -218,7 +218,7 @@
- Anthony Underwood. Contributor.
+
Anthony Underwood. Contributor.
@@ -273,7 +273,7 @@ Antimicrobial Resistance Data. Journal of Statistical Software (accepted for pub
diff --git a/docs/index.html b/docs/index.html
index 8f0ab1d5..3a76e30f 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -47,7 +47,7 @@
AMR (for R)
- 1.8.0
+ 1.8.0.9002
@@ -214,7 +214,7 @@
# AMR works great with dplyr, but it's not required or neccesary
-library(AMR)
+library(AMR)
library(dplyr)
example_isolates %>%
@@ -340,7 +340,7 @@
The development of this package is part of, related to, or made possible by:
-
+
-
Last updated: 26 February 2022
+
Last updated: 2 March 2022
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.
-
Changed
+
Changed
Support for antibiotic interpretations of the MIPS laboratory system: "U" for S (‘susceptible urine’), "D" for I (‘susceptible dose-dependent’)
-
Improved algorithm of as.mo(), especially for ignoring non-taxonomic text, such as:
@@ -172,9 +172,10 @@
mo_name("methicillin-resistant S. aureus (MRSA)")
#> [1] "Staphylococcus aureus"
+
More informative warning messages
-
Other
+
Other
- Fix for unit testing on R 3.3
- Fix for size of some image elements, as requested by CRAN
diff --git a/docs/survey.html b/docs/survey.html
index 54c019b0..e7bc3fe5 100644
--- a/docs/survey.html
+++ b/docs/survey.html
@@ -17,7 +17,7 @@
AMR (for R)
- 1.8.0
+ 1.8.0.9002
