From ec310ed76b69e8efaf3f03d52b9741a063cb715f Mon Sep 17 00:00:00 2001 From: Claude Date: Thu, 19 Mar 2026 07:24:09 +0000 Subject: [PATCH] Apply {.topic}, {.cls}, and {.field} markup in sir.R messaging - '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 --- R/sir.R | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/R/sir.R b/R/sir.R index ea8aac961..502bb1d92 100755 --- a/R/sir.R +++ b/R/sir.R @@ -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) } } }