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auto-remove missing ABs in antibiogram()
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Package: AMR
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Package: AMR
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Version: 1.8.2.9139
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Version: 1.8.2.9140
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Date: 2023-02-22
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Date: 2023-02-22
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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Description: Functions to simplify and standardise antimicrobial resistance (AMR)
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2
NEWS.md
2
NEWS.md
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# AMR 1.8.2.9139
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# AMR 1.8.2.9140
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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*(this beta version will eventually become v2.0! We're happy to reach a new major milestone soon!)*
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@ -313,14 +313,18 @@ antibiogram <- function(x,
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df_ab <- get_column_abx(x, verbose = FALSE, info = FALSE)
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df_ab <- get_column_abx(x, verbose = FALSE, info = FALSE)
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# get antibiotics from user
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# get antibiotics from user
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user_ab <- suppressMessages(suppressWarnings(lapply(antibiotics, as.ab, flag_multiple_results = FALSE, info = FALSE)))
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user_ab <- suppressMessages(suppressWarnings(lapply(antibiotics, as.ab, flag_multiple_results = FALSE, info = FALSE)))
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user_ab <- lapply(user_ab, function(x) unname(df_ab[match(x, names(df_ab))]))
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non_existing <- character(0)
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user_ab <- lapply(user_ab, function(x) {
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out <- unname(df_ab[match(x, names(df_ab))])
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non_existing <<- c(non_existing, x[is.na(out) & !is.na(x)])
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# remove non-existing columns
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# remove non-existing columns
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# non_existing <- unlist(antibiotics)[is.na(unlist(abx_ab))]
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out[!is.na(out)]
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# if (length(non_existing) > 0) {
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})
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# warning_("The following antibiotics were not available and ignored: ", vector_and(non_existing, sort = FALSE))
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user_ab <- user_ab[unlist(lapply(user_ab, length)) > 0]
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# abx_user <- Map(antibiotics, abx_user, f = function(input, ab) input[!is.na(ab)])
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# }
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if (length(non_existing) > 0) {
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warning_("The following antibiotics were not available and ignored: ", vector_and(ab_name(non_existing, language = NULL, tolower = TRUE), quotes = FALSE))
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}
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# make list unique
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# make list unique
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antibiotics <- unique(user_ab)
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antibiotics <- unique(user_ab)
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2
index.md
2
index.md
@ -115,7 +115,7 @@ Like many other functions in this package, `antibiogram()` comes with support fo
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```r
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```r
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antibiogram(example_isolates,
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antibiogram(example_isolates,
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antibiotics = c("CIP", "TOB", "GEN"),
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antibiotics = c("cipro", "tobra", "genta"), # any arbitrary name or code will work
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mo_transform = "gramstain",
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mo_transform = "gramstain",
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ab_transform = "name",
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ab_transform = "name",
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language = "uk") # Ukrainian
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language = "uk") # Ukrainian
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