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@ -324,7 +324,7 @@ warning_ <- function(...,
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# - adds the function name where the error was thrown
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# - wraps text to never break lines within words
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stop_ <- function(..., call = TRUE) {
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msg <- word_wrap(..., add_fn = list(), as_note = FALSE)
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msg <- paste0(c(...), collapse = "")
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if (!isFALSE(call)) {
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if (isTRUE(call)) {
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call <- as.character(sys.call(-1)[1])
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@ -334,6 +334,7 @@ stop_ <- function(..., call = TRUE) {
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}
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msg <- paste0("in ", call, "(): ", msg)
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}
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msg <- word_wrap(msg, add_fn = list(), as_note = FALSE)
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stop(msg, call. = FALSE)
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}
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@ -409,6 +410,7 @@ dataset_UTF8_to_ASCII <- function(df) {
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df
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}
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# for eucast_rules() and mdro(), creates markdown output with URLs and names
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create_ab_documentation <- function(ab) {
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ab_names <- ab_name(ab, language = NULL, tolower = TRUE)
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ab <- ab[order(ab_names)]
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@ -50,7 +50,7 @@
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#' All isolates with a microbial ID of `NA` will be excluded as first isolate.
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#'
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#' ### Why this is so important
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#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [(ref)](https:/pubmed.ncbi.nlm.nih.gov/17304462/). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all *S. aureus* isolates would be overestimated, because you included this MRSA more than once. It would be [selection bias](https://en.wikipedia.org/wiki/Selection_bias).
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#' To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [(Hindler *et al.* 2007)](https://pubmed.ncbi.nlm.nih.gov/17304462/). If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all *S. aureus* isolates would be overestimated, because you included this MRSA more than once. It would be [selection bias](https://en.wikipedia.org/wiki/Selection_bias).
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#'
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#' ### `filter_*()` shortcuts
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#'
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@ -60,6 +60,7 @@
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#'
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#' ```
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#' x[first_isolate(x, ...), ]
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#'
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#' x %>% filter(first_isolate(x, ...))
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#' ```
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#'
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