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completely updated antibiotics

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dr. M.S. (Matthijs) Berends
2022-10-30 14:31:45 +01:00
parent 3d9faf89cf
commit d40e0ef20b
60 changed files with 102028 additions and 95116 deletions
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12
man/proportion.Rd
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@ -165,12 +165,14 @@ This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{su
resistance(example_isolates$AMX)
rsi_confidence_interval(example_isolates$AMX)
rsi_confidence_interval(example_isolates$AMX,
confidence_level = 0.975)
confidence_level = 0.975
)
# determines \%S+I:
susceptibility(example_isolates$AMX)
rsi_confidence_interval(example_isolates$AMX,
ab_result = c("S", "I"))
ab_result = c("S", "I")
)
# be more specific
proportion_S(example_isolates$AMX)
@ -182,17 +184,14 @@ proportion_R(example_isolates$AMX)
# dplyr -------------------------------------------------------------
\donttest{
if (require("dplyr")) {
example_isolates \%>\%
group_by(ward) \%>\%
summarise(
r = resistance(CIP),
n = n_rsi(CIP)
) # n_rsi works like n_distinct in dplyr, see ?n_rsi
}
if (require("dplyr")) {
example_isolates \%>\%
group_by(ward) \%>\%
summarise(
@ -200,7 +199,6 @@ if (require("dplyr")) {
ci_min = rsi_confidence_interval(CIP, side = "min"),
ci_max = rsi_confidence_interval(CIP, side = "max"),
)
}
if (require("dplyr")) {
@ -212,10 +210,8 @@ if (require("dplyr")) {
c(aminoglycosides(), carbapenems()),
resistance
)
}
if (require("dplyr")) {
example_isolates \%>\%
group_by(ward) \%>\%
summarise(