diff --git a/.github/workflows/renew-gpt-training-data.yml b/.github/workflows/renew-gpt-training-data.yml index 5d12b9b7a..d599a1fc6 100644 --- a/.github/workflows/renew-gpt-training-data.yml +++ b/.github/workflows/renew-gpt-training-data.yml @@ -35,7 +35,7 @@ on: name: Publish GPT Training Data to GitHub jobs: - update-pypi: + update-amr-assistant: runs-on: ubuntu-latest env: diff --git a/DESCRIPTION b/DESCRIPTION index 7d6eadaa0..ba4ad1601 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 2.1.1.9254 +Version: 2.1.1.9255 Date: 2025-04-26 Title: Antimicrobial Resistance Data Analysis Description: Functions to simplify and standardise antimicrobial resistance (AMR) diff --git a/NEWS.md b/NEWS.md index 086fa3aeb..11c93d263 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 2.1.1.9254 +# AMR 2.1.1.9255 *(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! Install this beta using [the instructions here](https://amr-for-r.org/#get-this-package).)* diff --git a/R/sir.R b/R/sir.R index 6d653ae63..f4a31244f 100755 --- a/R/sir.R +++ b/R/sir.R @@ -146,7 +146,7 @@ #' options(AMR_breakpoint_type = "animal") #' ``` #' -#' ###### TODO #187 When applying veterinary breakpoints (by setting `host` or by setting `breakpoint_type = "animal"`), the [CLSI VET09 guideline](https://clsi.org/standards/products/veterinary-medicine/documents/vet09/) will be applied to cope with missing animal species-specific breakpoints. +###### TODO #187 When applying veterinary breakpoints (by setting `host` or by setting `breakpoint_type = "animal"`), the [CLSI VET09 guideline](https://clsi.org/standards/products/veterinary-medicine/documents/vet09/) will be applied to cope with missing animal species-specific breakpoints. #' #' ### After Interpretation #' @@ -994,12 +994,7 @@ as.sir.data.frame <- function(x, sir_logs_all <- lapply(result_list, function(x) x$log) sir_logs_all <- Filter(Negate(is.null), sir_logs_all) # remove NULLs early if (length(sir_logs_all) > 0) { - rbindlist <- import_fn("rbindlist", "data.table", error_on_fail = FALSE) - if (!is.null(rbindlist)) { - sir_logs_all <- rbindlist(sir_logs_all, fill = TRUE, ignore.attr = TRUE) - } else { - sir_logs_all <- do.call(rbind, sir_logs_all) - } + sir_logs_all <- do.call(rbind_AMR, sir_logs_all) AMR_env$sir_interpretation_history <- rbind_AMR(AMR_env$sir_interpretation_history, sir_logs_all) } @@ -1857,6 +1852,7 @@ sir_interpretation_history <- function(clean = FALSE) { meet_criteria(clean, allow_class = "logical", has_length = 1) out <- AMR_env$sir_interpretation_history out$outcome <- as.sir(out$outcome) + out$site <- as.character(out$site) if (isTRUE(clean)) { AMR_env$sir_interpretation_history <- AMR_env$sir_interpretation_history[0, , drop = FALSE] } diff --git a/man/as.sir.Rd b/man/as.sir.Rd index 77e68c048..7b3a8a195 100644 --- a/man/as.sir.Rd +++ b/man/as.sir.Rd @@ -231,9 +231,6 @@ Regarding choice of veterinary guidelines, these might be the best options to se \if{html}{\out{
}}\preformatted{ options(AMR_guideline = "CLSI") options(AMR_breakpoint_type = "animal") }\if{html}{\out{
}} -\subsection{TODO #187 When applying veterinary breakpoints (by setting \code{host} or by setting \code{breakpoint_type = "animal"}), the \href{https://clsi.org/standards/products/veterinary-medicine/documents/vet09/}{CLSI VET09 guideline} will be applied to cope with missing animal species-specific breakpoints.}{ -} - } \subsection{After Interpretation}{