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(v2.1.1.9050) vctrs fix for sir
, small documentation fixes
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@ -251,6 +251,51 @@ summary(example_isolates) # see all SIR results at a glance
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# For INTERPRETING disk diffusion and MIC values -----------------------
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\donttest{
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## Using dplyr -------------------------------------------------
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if (require("dplyr")) {
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# approaches that all work without additional arguments:
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df \%>\% mutate_if(is.mic, as.sir)
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df \%>\% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
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df \%>\% mutate(across(where(is.mic), as.sir))
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df \%>\% mutate_at(vars(AMP:TOB), as.sir)
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df \%>\% mutate(across(AMP:TOB, as.sir))
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# approaches that all work with additional arguments:
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df \%>\% mutate_if(is.mic, as.sir, mo = "column1", guideline = "CLSI")
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df \%>\% mutate(across(where(is.mic),
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function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
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df \%>\% mutate_at(vars(AMP:TOB), as.sir, mo = "column1", guideline = "CLSI")
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df \%>\% mutate(across(AMP:TOB,
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function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
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# for veterinary breakpoints, add 'host':
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df \%>\% mutate_if(is.mic, as.sir, guideline = "CLSI", host = "species_column")
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df \%>\% mutate_if(is.mic, as.sir, guideline = "CLSI", host = "horse")
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df \%>\% mutate(across(where(is.mic),
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function(x) as.sir(x, guideline = "CLSI", host = "species_column")))
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df \%>\% mutate_at(vars(AMP:TOB), as.sir, guideline = "CLSI", host = "species_column")
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df \%>\% mutate(across(AMP:TOB,
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function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
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# to include information about urinary tract infections (UTI)
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data.frame(mo = "E. coli",
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nitrofuratoin = c("<= 2", 32),
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from_the_bladder = c(TRUE, FALSE)) \%>\%
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as.sir(uti = "from_the_bladder")
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data.frame(mo = "E. coli",
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nitrofuratoin = c("<= 2", 32),
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specimen = c("urine", "blood")) \%>\%
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as.sir() # automatically determines urine isolates
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df \%>\%
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mutate_at(vars(AMP:TOB), as.sir, mo = "E. coli", uti = TRUE)
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}
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## Using base R ------------------------------------------------
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# a whole data set, even with combined MIC values and disk zones
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df <- data.frame(
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microorganism = "Escherichia coli",
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@ -280,36 +325,6 @@ as.sir(
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guideline = "EUCAST"
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)
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\donttest{
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# the dplyr way
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if (require("dplyr")) {
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df \%>\% mutate_if(is.mic, as.sir)
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df \%>\% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
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df \%>\% mutate(across(where(is.mic), as.sir))
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df \%>\% mutate_at(vars(AMP:TOB), as.sir)
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df \%>\% mutate(across(AMP:TOB, as.sir))
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df \%>\%
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mutate_at(vars(AMP:TOB), as.sir, mo = "microorganism")
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# to include information about urinary tract infections (UTI)
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data.frame(
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mo = "E. coli",
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NIT = c("<= 2", 32),
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from_the_bladder = c(TRUE, FALSE)
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) \%>\%
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as.sir(uti = "from_the_bladder")
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data.frame(
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mo = "E. coli",
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NIT = c("<= 2", 32),
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specimen = c("urine", "blood")
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) \%>\%
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as.sir() # automatically determines urine isolates
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df \%>\%
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mutate_at(vars(AMP:TOB), as.sir, mo = "E. coli", uti = TRUE)
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}
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# For CLEANING existing SIR values ------------------------------------
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