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(v0.7.1.9063) septic_patients -> example_isolates

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dr. M.S. (Matthijs) Berends
2019-08-27 16:45:42 +02:00
parent 7a6fce4eb8
commit 93be16484b
92 changed files with 1143 additions and 818 deletions
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38
man/count.Rd
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@ -122,29 +122,29 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
}
\examples{
# septic_patients is a data set available in the AMR package. It is true, genuine data.
?septic_patients
# example_isolates is a data set available in the AMR package.
?example_isolates
# Count resistant isolates
count_R(septic_patients$AMX)
count_IR(septic_patients$AMX)
count_R(example_isolates$AMX)
count_IR(example_isolates$AMX)
# Or susceptible isolates
count_S(septic_patients$AMX)
count_SI(septic_patients$AMX)
count_S(example_isolates$AMX)
count_SI(example_isolates$AMX)
# Count all available isolates
count_all(septic_patients$AMX)
n_rsi(septic_patients$AMX)
count_all(example_isolates$AMX)
n_rsi(example_isolates$AMX)
# Since n_rsi counts available isolates, you can
# calculate back to count e.g. non-susceptible isolates.
# This results in the same:
count_SI(septic_patients$AMX)
portion_SI(septic_patients$AMX) * n_rsi(septic_patients$AMX)
count_SI(example_isolates$AMX)
portion_SI(example_isolates$AMX) * n_rsi(example_isolates$AMX)
library(dplyr)
septic_patients \%>\%
example_isolates \%>\%
group_by(hospital_id) \%>\%
summarise(R = count_R(CIP),
I = count_I(CIP),
@ -156,24 +156,24 @@ septic_patients \%>\%
# Count co-resistance between amoxicillin/clav acid and gentamicin,
# so we can see that combination therapy does a lot more than mono therapy.
# Please mind that `portion_SI` calculates percentages right away instead.
count_SI(septic_patients$AMC) # 1433
count_all(septic_patients$AMC) # 1879
count_SI(example_isolates$AMC) # 1433
count_all(example_isolates$AMC) # 1879
count_SI(septic_patients$GEN) # 1399
count_all(septic_patients$GEN) # 1855
count_SI(example_isolates$GEN) # 1399
count_all(example_isolates$GEN) # 1855
with(septic_patients,
with(example_isolates,
count_SI(AMC, GEN)) # 1764
with(septic_patients,
with(example_isolates,
n_rsi(AMC, GEN)) # 1936
# Get portions S/I/R immediately of all rsi columns
septic_patients \%>\%
example_isolates \%>\%
select(AMX, CIP) \%>\%
count_df(translate = FALSE)
# It also supports grouping variables
septic_patients \%>\%
example_isolates \%>\%
select(hospital_id, AMX, CIP) \%>\%
group_by(hospital_id) \%>\%
count_df(translate = FALSE)