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(v2.1.1.9163) cleanup

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dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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112
man/as.sir.Rd
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@ -258,69 +258,97 @@ if (require("dplyr")) {
df_wide \%>\% mutate(across(where(is.mic), as.sir))
df_wide \%>\% mutate_at(vars(amoxicillin:tobra), as.sir)
df_wide \%>\% mutate(across(amoxicillin:tobra, as.sir))
# approaches that all work with additional arguments:
df_long \%>\%
# given a certain data type, e.g. MIC values
mutate_if(is.mic, as.sir,
mo = "bacteria",
ab = "antibiotic",
guideline = "CLSI")
mo = "bacteria",
ab = "antibiotic",
guideline = "CLSI"
)
df_long \%>\%
mutate(across(where(is.mic),
function(x) as.sir(x,
mo = "bacteria",
ab = "antibiotic",
guideline = "CLSI")))
mutate(across(
where(is.mic),
function(x) {
as.sir(x,
mo = "bacteria",
ab = "antibiotic",
guideline = "CLSI"
)
}
))
df_wide \%>\%
# given certain columns, e.g. from 'cipro' to 'genta'
mutate_at(vars(cipro:genta), as.sir,
mo = "bacteria",
guideline = "CLSI")
mo = "bacteria",
guideline = "CLSI"
)
df_wide \%>\%
mutate(across(cipro:genta,
function(x) as.sir(x,
mo = "bacteria",
guideline = "CLSI")))
mutate(across(
cipro:genta,
function(x) {
as.sir(x,
mo = "bacteria",
guideline = "CLSI"
)
}
))
# for veterinary breakpoints, add 'host':
df_long$animal_species <- c("cats", "dogs", "horses", "cattle")
df_long \%>\%
# given a certain data type, e.g. MIC values
mutate_if(is.mic, as.sir,
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI")
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI"
)
df_long \%>\%
mutate(across(where(is.mic),
function(x) as.sir(x,
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI")))
mutate(across(
where(is.mic),
function(x) {
as.sir(x,
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI"
)
}
))
df_wide \%>\%
mutate_at(vars(cipro:genta), as.sir,
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI")
mo = "bacteria",
ab = "antibiotic",
host = "animal_species",
guideline = "CLSI"
)
df_wide \%>\%
mutate(across(cipro:genta,
function(x) as.sir(x,
mo = "bacteria",
host = "animal_species",
guideline = "CLSI")))
mutate(across(
cipro:genta,
function(x) {
as.sir(x,
mo = "bacteria",
host = "animal_species",
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)) \%>\%
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")) \%>\%
data.frame(
mo = "E. coli",
nitrofuratoin = c("<= 2", 32),
specimen = c("urine", "blood")
) \%>\%
as.sir() # automatically determines urine isolates
df_wide \%>\%