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Apply {.topic}, {.cls}, and {.field} markup in sir.R messaging

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- 'clinical_breakpoints' (dataset): {.code} -> {.topic [clinical_breakpoints](AMR::clinical_breakpoints)}
- "is of class" context: extract bad_col/bad_cls/exp_cls vars and use {.cls} + {.field} in glue syntax
- Column references in as.sir() messages: font_bold(col) with surrounding quotes -> {.field {col}}

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-19 07:24:09 +00:00
parent 3e4983ff93
commit ec310ed76b
1 changed files with 8 additions and 6 deletions
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14
R/sir.R
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@@ -835,8 +835,7 @@ as.sir.data.frame <- function(x,
message_(
"Assuming value", plural[1], " ",
vector_and(col_values, quotes = TRUE),
" in column '", font_bold(col_specimen),
"' reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
" in column {.field {col_specimen}} reflect", plural[2], " ", plural[3], "urinary tract infection", plural[1],
".\n Use `as.sir(uti = FALSE)` to prevent this."
)
}
@@ -975,7 +974,7 @@ as.sir.data.frame <- function(x,
if (!all(x[, ab, drop = TRUE] %in% c("S", "SDD", "I", "R", "NI", NA), na.rm = TRUE)) {
show_message <- TRUE
if (isTRUE(info)) {
message_("Cleaning values in column '", font_bold(ab), "' (",
message_("Cleaning values in column {.field {ab}} (",
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE, info = info), ")... ",
appendLF = FALSE,
@@ -985,7 +984,7 @@ as.sir.data.frame <- function(x,
} else if (!is.sir(x.bak[, ab, drop = TRUE])) {
show_message <- TRUE
if (isTRUE(info)) {
message_("Assigning class {.cls sir} to already clean column '", font_bold(ab), "' (",
message_("Assigning class {.cls sir} to already clean column {.field {ab}} (",
ifelse(ab_coerced != toupper(ab), paste0(ab_coerced, ", "), ""),
ab_name(ab_coerced, tolower = TRUE, language = NULL, info = info), ")... ",
appendLF = FALSE,
@@ -2227,10 +2226,13 @@ check_reference_data <- function(reference_data, .call_depth) {
class_sir <- vapply(FUN.VALUE = character(1), AMR::clinical_breakpoints, function(x) paste0("<", class(x), ">", collapse = " and "))
class_ref <- vapply(FUN.VALUE = character(1), reference_data, function(x) paste0("<", class(x), ">", collapse = " and "))
if (!all(names(class_sir) == names(class_ref))) {
stop_("{.arg reference_data} must have the same column names as the {.code clinical_breakpoints} data set.", call = .call_depth)
stop_("{.arg reference_data} must have the same column names as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set.", call = .call_depth)
}
if (!all(class_sir == class_ref)) {
stop_("{.arg reference_data} must be the same structure as the {.code clinical_breakpoints} data set. Column '", names(class_ref[class_sir != class_ref][1]), "' is of class ", class_ref[class_sir != class_ref][1], ", but should be of class ", class_sir[class_sir != class_ref][1], ".", call = .call_depth)
bad_col <- names(class_ref[class_sir != class_ref][1])
bad_cls <- gsub("<|>", "", class_ref[class_sir != class_ref][1])
exp_cls <- gsub("<|>", "", class_sir[class_sir != class_ref][1])
stop_("{.arg reference_data} must be the same structure as the {.topic [clinical_breakpoints](AMR::clinical_breakpoints)} data set. Column {.field {bad_col}} is of class {.cls {bad_cls}}, but should be of class {.cls {exp_cls}}", call = .call_depth)
}
}
}