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(v2.1.1.9225) fix geom_hline()/_vline() in MIC plotting, add EUCAT 1.2 in full, add London contribs, fix mo codes, add Kleb pneu complex
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@ -33,7 +33,7 @@ is.sir(x)
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is_sir_eligible(x, threshold = 0.05)
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\method{as.sir}{default}(x, S = "^(S|U)+$", I = "^(I)+$", R = "^(R)+$",
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NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", ...)
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NI = "^(N|NI|V)+$", SDD = "^(SDD|D|H)+$", info = TRUE, ...)
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\method{as.sir}{mic}(x, mo = NULL, ab = deparse(substitute(x)),
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guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
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@ -44,7 +44,7 @@ is_sir_eligible(x, threshold = 0.05)
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FALSE), include_screening = getOption("AMR_include_screening", FALSE),
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
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verbose = FALSE, conserve_capped_values = NULL, ...)
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verbose = FALSE, info = TRUE, conserve_capped_values = NULL, ...)
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\method{as.sir}{disk}(x, mo = NULL, ab = deparse(substitute(x)),
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guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
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@ -54,7 +54,7 @@ is_sir_eligible(x, threshold = 0.05)
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FALSE), include_screening = getOption("AMR_include_screening", FALSE),
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
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verbose = FALSE, ...)
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verbose = FALSE, info = TRUE, ...)
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\method{as.sir}{data.frame}(x, ..., col_mo = NULL,
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guideline = getOption("AMR_guideline", "EUCAST"), uti = NULL,
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@ -65,7 +65,7 @@ is_sir_eligible(x, threshold = 0.05)
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FALSE), include_screening = getOption("AMR_include_screening", FALSE),
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include_PKPD = getOption("AMR_include_PKPD", TRUE),
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breakpoint_type = getOption("AMR_breakpoint_type", "human"), host = NULL,
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verbose = FALSE, conserve_capped_values = NULL)
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verbose = FALSE, info = TRUE, conserve_capped_values = NULL)
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sir_interpretation_history(clean = FALSE)
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}
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@ -78,6 +78,8 @@ sir_interpretation_history(clean = FALSE)
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\item{S, I, R, NI, SDD}{a case-independent \link[base:regex]{regular expression} to translate input to this result. This regular expression will be run \emph{after} all non-letters and whitespaces are removed from the input.}
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\item{info}{a \link{logical} to print information about the process}
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\item{mo}{a vector (or column name) with \link{character}s that can be coerced to valid microorganism codes with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically}
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\item{ab}{a vector (or column name) with \link{character}s that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
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