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(v2.1.1.9050) vctrs fix for sir, small documentation fixes

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dr. M.S. (Matthijs) Berends
2024-06-15 15:33:49 +02:00
parent 9bf7584d58
commit bdbf5198a2
15 changed files with 248 additions and 165 deletions
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75
man/as.sir.Rd
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@ -251,6 +251,51 @@ summary(example_isolates) # see all SIR results at a glance
# For INTERPRETING disk diffusion and MIC values -----------------------
\donttest{
## Using dplyr -------------------------------------------------
if (require("dplyr")) {
# approaches that all work without additional arguments:
df \%>\% mutate_if(is.mic, as.sir)
df \%>\% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
df \%>\% mutate(across(where(is.mic), as.sir))
df \%>\% mutate_at(vars(AMP:TOB), as.sir)
df \%>\% mutate(across(AMP:TOB, as.sir))
# approaches that all work with additional arguments:
df \%>\% mutate_if(is.mic, as.sir, mo = "column1", guideline = "CLSI")
df \%>\% mutate(across(where(is.mic),
function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
df \%>\% mutate_at(vars(AMP:TOB), as.sir, mo = "column1", guideline = "CLSI")
df \%>\% mutate(across(AMP:TOB,
function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
# for veterinary breakpoints, add 'host':
df \%>\% mutate_if(is.mic, as.sir, guideline = "CLSI", host = "species_column")
df \%>\% mutate_if(is.mic, as.sir, guideline = "CLSI", host = "horse")
df \%>\% mutate(across(where(is.mic),
function(x) as.sir(x, guideline = "CLSI", host = "species_column")))
df \%>\% mutate_at(vars(AMP:TOB), as.sir, guideline = "CLSI", host = "species_column")
df \%>\% mutate(across(AMP:TOB,
function(x) as.sir(x, mo = "column1", guideline = "CLSI")))
# to include information about urinary tract infections (UTI)
data.frame(mo = "E. coli",
nitrofuratoin = c("<= 2", 32),
from_the_bladder = c(TRUE, FALSE)) \%>\%
as.sir(uti = "from_the_bladder")
data.frame(mo = "E. coli",
nitrofuratoin = c("<= 2", 32),
specimen = c("urine", "blood")) \%>\%
as.sir() # automatically determines urine isolates
df \%>\%
mutate_at(vars(AMP:TOB), as.sir, mo = "E. coli", uti = TRUE)
}
## Using base R ------------------------------------------------
# a whole data set, even with combined MIC values and disk zones
df <- data.frame(
microorganism = "Escherichia coli",
@ -280,36 +325,6 @@ as.sir(
guideline = "EUCAST"
)
\donttest{
# the dplyr way
if (require("dplyr")) {
df \%>\% mutate_if(is.mic, as.sir)
df \%>\% mutate_if(function(x) is.mic(x) | is.disk(x), as.sir)
df \%>\% mutate(across(where(is.mic), as.sir))
df \%>\% mutate_at(vars(AMP:TOB), as.sir)
df \%>\% mutate(across(AMP:TOB, as.sir))
df \%>\%
mutate_at(vars(AMP:TOB), as.sir, mo = "microorganism")
# to include information about urinary tract infections (UTI)
data.frame(
mo = "E. coli",
NIT = c("<= 2", 32),
from_the_bladder = c(TRUE, FALSE)
) \%>\%
as.sir(uti = "from_the_bladder")
data.frame(
mo = "E. coli",
NIT = c("<= 2", 32),
specimen = c("urine", "blood")
) \%>\%
as.sir() # automatically determines urine isolates
df \%>\%
mutate_at(vars(AMP:TOB), as.sir, mo = "E. coli", uti = TRUE)
}
# For CLEANING existing SIR values ------------------------------------