@@ -24,7 +24,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
< a class = "navbar-brand me-2" href = "../index.html" > AMR (for R)< / a >
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< small class = "nav-text text-muted me-auto" data-bs-toggle = "tooltip" data-bs-placement = "bottom" title = "" > 2.1.1.9054 < / small >
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@@ -574,32 +574,89 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # For INTERPRETING disk diffusion and MIC values -----------------------< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # example data sets, with combined MIC values and disk zones< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_wide< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > microorganism < span class = "op" > =< / span > < span class = "st" > "Escherichia coli"< / span > ,< / span > < / span >
< span class = "r-in" > < span > AMP < span class = "op" > =< / span > < span class = "fu" > < a href = "as.mic.html" > as.mic< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 8< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > CIP < span class = "op" > =< / span > < span class = "fu" > < a href = "as.mic.html" > as.mic< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 0.256< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > GEN < span class = "op" > =< / span > < span class = "fu" > < a href = "as.disk.html" > as.disk< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 18< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > TOB < span class = "op" > =< / span > < span class = "fu" > < a href = "as.disk.html" > as.disk< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 16< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > ERY < span class = "op" > =< / span > < span class = "st" > "R"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_long< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > bacteria < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/rep.html" class = "external-link" > rep< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "Escherichia coli"< / span > , < span class = "fl" > 3< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > antibiotic < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "amoxicillin"< / span > , < span class = "st" > "cipro"< / span > , < span class = "st" > "tobra"< / span > , < span class = "st" > "genta"< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > mics < span class = "op" > =< / span > < span class = "fu" > < a href = "as.mic.html" > as.mic< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 0.01< / span > , < span class = "fl" > 1< / span > , < span class = "fl" > 4< / span > , < span class = "fl" > 8< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > disks < span class = "op" > =< / span > < span class = "fu" > < a href = "as.disk.html" > as.disk< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 6< / span > , < span class = "fl" > 10< / span > , < span class = "fl" > 14< / span > , < span class = "fl" > 18< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-err co" > < span class = "r-pr" > #> < / span > < span class = "error" > Error in data.frame(bacteria = rep("Escherichia coli", 3), antibiotic = c("amoxicillin", "cipro", "tobra", "genta"), mics = as.mic(c(0.01, 1, 4, 8)), disks = as.disk(c(6, 10, 14, 18))):< / span > arguments imply differing number of rows: 3, 4< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # \donttest{< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > ## Using dplyr -------------------------------------------------< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > if< / span > < span class = "op" > (< / span > < span class = "kw" > < a href = "https://rdrr.io/r/base/library.html" class = "external-link" > require< / a > < / span > < span class = "op" > (< / span > < span class = "st" > < a href = "https://dplyr.tidyverse.org" class = "external-link" > "dplyr"< / a > < / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > {< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # approaches that all work without additional arguments:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_if< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.mic< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_if< / a > < / span > < span class = "op" > (< / span > < span class = "kw" > function< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > < a href = "as.mic.html" > is.mic< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "op" > |< / span > < span class = "fu" > < a href = "as.disk.html" > is.disk< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://tidyselect.r-lib.org/reference/where.html" class = "external-link" > where< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.mic< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_at< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/vars.html" class = "external-link" > vars< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_wide < / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_if< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.mic< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_wide < / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_if< / a > < / span > < span class = "op" > (< / span > < span class = "kw" > function< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > < a href = "as.mic.html" > is.mic< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "op" > |< / span > < span class = "fu" > < a href = "as.disk.html" > is.disk< / a > < / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_wide < / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://tidyselect.r-lib.org/reference/where.html" class = "external-link" > where< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.mic< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_wide < / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_at< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/vars.html" class = "external-link" > vars< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_wide < / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > , < span class = "va" > as.sir< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # approaches that all work with additional arguments:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_if< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.mic< / span > , < span class = "va" > as.sir< / span > , mo < span class = "op" > =< / span > < span class = "st" > "column1"< / span > , guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op " > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://tidyselect.r-lib.org/reference/where.html" class = "external-link" > where< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.mic< / span > < span class = "op" > )< / span > , < / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > function< / span > < span class = "op " > ( < / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , mo < span class = "op" > =< / span > < span class = "st" > "column1"< / span > , guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > ) < / span > < span class = "op " > ) < / span > < span class = "op " > ) < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_at< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/vars.html" class = "external-link" > vars< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > , mo < span class = "op" > =< / span > < span class = "st" > "column1"< / span > , guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > ( < / span > < span class = "va " > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB < / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > function< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , mo < span class = "op" > =< / span > < span class = "st" > "column1"< / span > , guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_long < / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "c o" > # given a certain data type, e.g. MIC values < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu " > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_if< / a > < / span > < span class = "op" > ( < / span > < span class = "va " > is.mic < / span > , < span class = "va " > as.sir < / span > , < / span > < / span >
< span class = "r-in" > < span > mo < span class = "op" > =< / span > < span class = "st" > "bacteria"< / span > , < / span > < / span >
< span class = "r-in" > < span > ab < span class = "op" > = < / span > < span class = "st " > "antibiotic" < / span > ,< / span > < / span >
< span class = "r-in" > < span > guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_long< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://tidyselect.r-lib.org/reference/where.html" class = "external-link" > where< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.mic< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > function< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo < span class = "op" > =< / span > < span class = "st" > "bacteria"< / span > ,< / span > < / span >
< span class = "r-in" > < span > ab < span class = "op" > =< / span > < span class = "st" > "antibiotic"< / span > ,< / span > < / span >
< span class = "r-in" > < span > guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_long< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # given certain columns, e.g. from AMP to TOB< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_at< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/vars.html" class = "external-link" > vars< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo < span class = "op" > =< / span > < span class = "st" > "bacteria"< / span > ,< / span > < / span >
< span class = "r-in" > < span > ab < span class = "op" > =< / span > < span class = "st" > "antibiotic"< / span > ,< / span > < / span >
< span class = "r-in" > < span > guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_long< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > function< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo < span class = "op" > =< / span > < span class = "st" > "bacteria"< / span > ,< / span > < / span >
< span class = "r-in" > < span > ab < span class = "op" > =< / span > < span class = "st" > "antibiotic"< / span > ,< / span > < / span >
< span class = "r-in" > < span > guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # for veterinary breakpoints, add 'host':< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link " > % &g t; %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all .html" class = "external-link" > mutate_if < / a > < / span > < span class = "op" > (< / span > < span class = "va " > is.mic< / span > , < span class = "va" > as.sir < / span > , guideline < span class = "op " > = < / span > < span class = "st" > "CLSI"< / span > , host < span class = "op" > = < / span > < span class = "st" > "species_column "< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_if< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.mic< / span > , < span class = "va" > as.sir< / span > , guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > , host < span class = "op" > =< / span > < span class = "st" > "horse"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op " > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://tidyselect.r-lib.org/reference/where.html" class = "external-link" > where< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.mic< / span > < span class = "op" > )< / span > , < / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > function< / span > < span class = "op " > ( < / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > , host < span class = "op" > = < / span > < span class = "st " > "species_column"< / span > < span class = "op" > ) < / span > < span class = "op " > )< / span > < span class = "op" > ) < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_at< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/vars.html" class = "external-link" > vars< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > , guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > , host < span class = "op" > =< / span > < span class = "st" > "species_column"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > ( < / span > < span class = "va " > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB < / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > function< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > , mo < span class = "op" > =< / span > < span class = "st" > "column1"< / span > , guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > ) < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_long < / span > < span class = "op" > $ < / span > < span class = "va" > animal_species< / span > < span class = "op " > &l t; - < / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c .html" class = "external-link" > c < / a > < / span > < span class = "op" > (< / span > < span class = "st " > "cats" < / span > , < span class = "st " > "dogs" < / span > , < span class = "st" > "horses" < / span > , < span class = "st" > "cattle "< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_long < / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "c o" > # given a certain data type, e.g. MIC values < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu " > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_if< / a > < / span > < span class = "op" > ( < / span > < span class = "va " > is.mic < / span > , < span class = "va " > as.sir < / span > , < / span > < / span >
< span class = "r-in" > < span > mo < span class = "op" > =< / span > < span class = "st" > "bacteria" < / span > , < / span > < / span >
< span class = "r-in" > < span > ab < span class = "op" > = < / span > < span class = "st " > "antibiotic" < / span > ,< / span > < / span >
< span class = "r-in" > < span > host < span class = "op" > =< / span > < span class = "st" > "animal_species" < / span > , < / span > < / span >
< span class = "r-in" > < span > guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_long< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://tidyselect.r-lib.org/reference/where.html" class = "external-link" > where< / a > < / span > < span class = "op" > (< / span > < span class = "va" > is.mic< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > function< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo < span class = "op" > =< / span > < span class = "st" > "bacteria"< / span > ,< / span > < / span >
< span class = "r-in" > < span > ab < span class = "op" > =< / span > < span class = "st" > "antibiotic"< / span > ,< / span > < / span >
< span class = "r-in" > < span > host < span class = "op" > =< / span > < span class = "st" > "animal_species"< / span > ,< / span > < / span >
< span class = "r-in" > < span > guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_long< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # given certain columns, e.g. from AMP to TOB< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_at< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/vars.html" class = "external-link" > vars< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo < span class = "op" > =< / span > < span class = "st" > "bacteria"< / span > ,< / span > < / span >
< span class = "r-in" > < span > ab < span class = "op" > =< / span > < span class = "st" > "antibiotic"< / span > ,< / span > < / span >
< span class = "r-in" > < span > host < span class = "op" > =< / span > < span class = "st" > "animal_species"< / span > ,< / span > < / span >
< span class = "r-in" > < span > guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_long< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate.html" class = "external-link" > mutate< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/across.html" class = "external-link" > across< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > ,< / span > < / span >
< span class = "r-in" > < span > < span class = "kw" > function< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > < span class = "op" > )< / span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "va" > x< / span > ,< / span > < / span >
< span class = "r-in" > < span > mo < span class = "op" > =< / span > < span class = "st" > "bacteria"< / span > ,< / span > < / span >
< span class = "r-in" > < span > ab < span class = "op" > =< / span > < span class = "st" > "antibiotic"< / span > ,< / span > < / span >
< span class = "r-in" > < span > host < span class = "op" > =< / span > < span class = "st" > "animal_species"< / span > ,< / span > < / span >
< span class = "r-in" > < span > guideline < span class = "op" > =< / span > < span class = "st" > "CLSI"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # to include information about urinary tract infections (UTI)< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > mo < span class = "op" > =< / span > < span class = "st" > "E. coli"< / span > ,< / span > < / span >
@@ -612,24 +669,78 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
< span class = "r-in" > < span > specimen < span class = "op" > =< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "urine"< / span > , < span class = "st" > "blood"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < span class = "co" > # automatically determines urine isolates< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df_wide < / span > < span class = "op" > < a href = "https://magrittr.tidyverse.org/reference/pipe.html" class = "external-link" > %> %< / a > < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/mutate_all.html" class = "external-link" > mutate_at< / a > < / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://dplyr.tidyverse.org/reference/vars.html" class = "external-link" > vars< / a > < / span > < span class = "op" > (< / span > < span class = "va" > AMP< / span > < span class = "op" > :< / span > < span class = "va" > TOB< / span > < span class = "op" > )< / span > , < span class = "va" > as.sir< / span > , mo < span class = "op" > =< / span > < span class = "st" > "E. coli"< / span > , uti < span class = "op" > =< / span > < span class = "cn" > TRUE< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > }< / span > < / span > < / span >
< span class = "r-err co" > < span class = "r-pr" > #> < / span > < span class = "error" > Error in UseMethod("tbl_vars"):< / span > no applicable method for 'tbl_vars' applied to an object of class "function"< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > all the details of the breakpoint interpretations.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: 'AMP' (ampicillin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: 'CIP' (ciprofloxacin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > NOTES < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > all the details of the breakpoint interpretations.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: 'AMP' (ampicillin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: 'CIP' (ciprofloxacin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > NOTES < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > all the details of the breakpoint interpretations.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: 'AMP' (ampicillin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: 'CIP' (ciprofloxacin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > NOTES < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > all the details of the breakpoint interpretations.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: 'AMP' (ampicillin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: 'CIP' (ciprofloxacin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > NOTES < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > all the details of the breakpoint interpretations.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: 'AMP' (ampicillin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: 'CIP' (ciprofloxacin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > NOTES < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > • Multiple breakpoints available for ciprofloxacin (CIP) in Escherichia coli - assuming body site 'Non-meningitis'.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: 'GEN' (gentamicin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting disk diffusion zones: 'TOB' (tobramycin) based on column< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > 'microorganism', EUCAST 2024...< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > OK < / span >
< span class = "r-err co" > < span class = "r-pr" > #> < / span > < span class = "error" > Error in eval(expr, envir, enclos):< / span > object 'df_long' not found< / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > ## Using base R ------------------------------------------------< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # a whole data set, even with combined MIC values and disk zones < / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "va" > df< / span > < span class = "op" > < -< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/data.frame.html" class = "external-link" > data.frame< / a > < / span > < span class = "op" > (< / span > < / span > < / span >
< span class = "r-in" > < span > microorganism < span class = "op" > =< / span > < span class = "st" > "Escherichia coli"< / span > ,< / span > < / span >
< span class = "r-in" > < span > AMP < span class = "op" > =< / span > < span class = "fu" > < a href = "as.mic.html" > as.mic< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 8< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > CIP < span class = "op" > =< / span > < span class = "fu" > < a href = "as.mic.html" > as.mic< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 0.256< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > GEN < span class = "op" > =< / span > < span class = "fu" > < a href = "as.disk.html" > as.disk< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 18< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > TOB < span class = "op" > =< / span > < span class = "fu" > < a href = "as.disk.html" > as.disk< / a > < / span > < span class = "op" > (< / span > < span class = "fl" > 16< / span > < span class = "op" > )< / span > ,< / span > < / span >
< span class = "r-in" > < span > ERY < span class = "op" > =< / span > < span class = "st" > "R"< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "va" > df< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "va" > df_wide< / span > < span class = "op" > ) < / span > < / span > < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > ℹ < / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > all the details of the breakpoint interpretations.< / span >
< span class = "r-msg co" > < span class = "r-pr" > #> < / span > Interpreting MIC values: column 'AMP' (ampicillin), EUCAST 2024...< / span >
@@ -650,22 +761,20 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "co" > # return a 'logbook' about the results:< / span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > sir_interpretation_history< / span > < span class = "op" > (< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 13 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # A tibble: 29 × < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > datetime index ab_given mo_given host_given ab mo < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > *< / span > < span style = "color: #949494; font-style: italic;" > < dttm> < / span > < span style = "color: #949494; font-style: italic;" > < int> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < chr> < / span > < span style = "color: #949494; font-style: italic;" > < ab> < / span > < span style = "color: #949494; font-style: italic;" > < mo> < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:27 < / span > 4 AMX B_STRPT… human AMX B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:27 < / span > 3 AMX B_STRPT… human AMX B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:27 < / span > 2 AMX B_STRPT… human AMX B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:26 < / span > 1 ampicil… Strep p… human AMP B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:26 < / span > 1 AMP Escheri… human AMP B_[ORD]_ENTRBCTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:26 < / span > 1 GEN Escheri… human GEN B_[ORD]_ENTRBCTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:27 < / span > 1 TOB Escheri… human TOB B_[ORD]_ENTRBCTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:27 < / span > 1 AMX B_STRPT… human AMX B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:27 < / span > 1 AMX B_STRPT… human AMX B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:31 < / span > 1 AMP Escheri… human AMP B_[ORD]_ENTRBCTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 11< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:32< / span > 1 CIP Escheri… human CIP B_[ORD]_ENTRBCTR < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 12< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:32< / span > 1 GEN Escheri… human GEN B_[ORD]_ENTRBCTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 13< / span > 2024-06-17 < span style = "color: #949494;" > 08:44:32< / span > 1 TOB Escheri… human TOB B_[ORD]_ENTRBCTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 1< / span > 2024-06-17 < span style = "color: #949494;" > 12:14:06 < / span > 4 AMX B_STRPT… human AMX B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 2< / span > 2024-06-17 < span style = "color: #949494;" > 12:14:06 < / span > 3 AMX B_STRPT… human AMX B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 3< / span > 2024-06-17 < span style = "color: #949494;" > 12:14:06 < / span > 2 AMX B_STRPT… human AMX B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 4< / span > 2024-06-17 < span style = "color: #949494;" > 12:14:05 < / span > 1 ampicil… Strep p… human AMP B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 5< / span > 2024-06-17 < span style = "color: #949494;" > 12:14:05 < / span > 1 AMP Escheri… human AMP B_[ORD]_ENTRBCTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 6< / span > 2024-06-17 < span style = "color: #949494;" > 12:14:05 < / span > 1 GEN Escheri… human GEN B_[ORD]_ENTRBCTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 7< / span > 2024-06-17 < span style = "color: #949494;" > 12:14:05 < / span > 1 TOB Escheri… human TOB B_[ORD]_ENTRBCTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 8< / span > 2024-06-17 < span style = "color: #949494;" > 12:14:06 < / span > 1 AMX B_STRPT… human AMX B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 9< / span > 2024-06-17 < span style = "color: #949494;" > 12:14:06 < / span > 1 AMX B_STRPT… human AMX B_STRPT_PNMN < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #BCBCBC;" > 10< / span > 2024-06-17 < span style = "color: #949494;" > 12:14:10 < / span > 1 AMP Escheri… human AMP B_[ORD]_ENTRBCTR< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # ℹ < chr> , method < chr> , input < dbl> , outcome < sir> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # notes < chr> , guideline < chr> , ref_table < chr> , uti < lgl> ,< / span > < / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > < span style = "color: #949494;" > # breakpoint_S_R < chr> < / span > < / span >
@@ -702,7 +811,7 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
< span class = "r-in" > < span > < span class = "co" > # For CLEANING existing SIR values ------------------------------------< / span > < / span > < / span >
< span class = "r-in" > < span > < / span > < / span >
< span class = "r-in" > < span > < span class = "fu" > as.sir< / span > < span class = "op" > (< / span > < span class = "fu" > < a href = "https://rdrr.io/r/base/c.html" class = "external-link" > c< / a > < / span > < span class = "op" > (< / span > < span class = "st" > "S"< / span > , < span class = "st" > "SDD"< / span > , < span class = "st" > "I"< / span > , < span class = "st" > "R"< / span > , < span class = "st" > "NI"< / span > , < span class = "st" > "A"< / span > , < span class = "st" > "B"< / span > , < span class = "st" > "C"< / span > < span class = "op" > )< / span > < span class = "op" > )< / span > < / span > < / span >
< span class = "r-wrn co" > < span class = "r-pr" > #> < / span > < span class = "warning" > Warning: < / span > in as.sir(): 3 results in column '28 ' truncated (38%) that were invalid< / span >
< span class = "r-wrn co" > < span class = "r-pr" > #> < / span > < span class = "warning" > Warning: < / span > in as.sir(): 3 results in column '30 ' truncated (38%) that were invalid< / span >
< span class = "r-wrn co" > < span class = "r-pr" > #> < / span > antimicrobial interpretations: "A", "B", and "C"< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > Class 'sir'< / span >
< span class = "r-out co" > < span class = "r-pr" > #> < / span > [1] S SDD I R NI < NA> < NA> < NA> < / span >
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