P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-03-19 13:42:25 +01:00
Code Releases Activity

Qualify all {.help} tags with AMR:: and convert backtick ?func references

Browse Source 
- Add AMR:: namespace prefix and trailing () to all {.help} cli markup
  so they render as clickable help links (e.g. {.help AMR::as.sir}())
- Convert `?funcname` backtick-quoted help references to {.help AMR::funcname}()
  in aa_helper_functions.R, custom_eucast_rules.R, interpretive_rules.R,
  key_antimicrobials.R, mo.R, plotting.R, resistance_predict.R, and sir.R
- Skipped `?proportion` in sir_calc.R as 'proportion' is not exported

https://claude.ai/code/session_01XHWLohiSTdZvCutwD7ag2b
This commit is contained in:
Claude
2026-03-18 20:06:52 +00:00
parent 4798d2c55e
commit 0cc154257a
14 changed files with 41 additions and 41 deletions
Download Patch File Download Diff File Expand all files Collapse all files

8
R/custom_eucast_rules.R
View File

@@ -150,15 +150,15 @@ custom_eucast_rules <- function(...) {
)
stop_if(
identical(dots, "error"),
"rules must be a valid formula inputs (e.g., using '~'), see `?custom_eucast_rules`"
"rules must be a valid formula inputs (e.g., using '~'), see {.help AMR::custom_eucast_rules}()"
)
n_dots <- length(dots)
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using `?custom_eucast_rules`.")
stop_if(n_dots == 0, "no custom rules were set. Please read the documentation using {.help AMR::custom_eucast_rules}().")
out <- vector("list", n_dots)
for (i in seq_len(n_dots)) {
stop_ifnot(
inherits(dots[[i]], "formula"),
"rule ", i, " must be a valid formula input (e.g., using '~'), see `?custom_eucast_rules`"
"rule ", i, " must be a valid formula input (e.g., using '~'), see {.help AMR::custom_eucast_rules}()"
)
# Query
@@ -180,7 +180,7 @@ custom_eucast_rules <- function(...) {
result <- dots[[i]][[3]]
stop_ifnot(
deparse(result) %like% "==",
"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see `?custom_eucast_rules`"
"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see {.help AMR::custom_eucast_rules}()"
)
result_group <- as.character(result)[[2]]
result_group <- as.character(str2lang(result_group))