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new antibiotics

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dr. M.S. (Matthijs) Berends
2019-05-10 16:44:59 +02:00
parent 73f1ee1159
commit 68cc7ef0d0
147 changed files with 6228 additions and 4187 deletions
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50
man/count.Rd
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@ -29,8 +29,8 @@ count_all(...)
n_rsi(...)
count_df(data, translate_ab = getOption("get_antibiotic_names",
"official"), combine_IR = FALSE)
count_df(data, translate_ab = "name", language = get_locale(),
combine_IR = FALSE)
}
\arguments{
\item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed.}
@ -39,7 +39,9 @@ count_df(data, translate_ab = getOption("get_antibiotic_names",
\item{data}{a \code{data.frame} containing columns with class \code{rsi} (see \code{\link{as.rsi}})}
\item{translate_ab}{a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations to, using \code{\link{abname}}. This can be set with \code{\link{getOption}("get_antibiotic_names")}.}
\item{translate_ab}{a column name of the \code{\link{antibiotics}} data set to translate the antibiotic abbreviations to, using \code{\link{ab_property}}}
\item{language}{language of the returned text, defaults to system language (see \code{\link{get_locale}}) and can also be set with \code{\link{getOption}("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
\item{combine_IR}{a logical to indicate whether all values of I and R must be merged into one, so the output only consists of S vs. IR (susceptible vs. non-susceptible)}
}
@ -68,55 +70,55 @@ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://
?septic_patients
# Count resistant isolates
count_R(septic_patients$amox)
count_IR(septic_patients$amox)
count_R(septic_patients$AMX)
count_IR(septic_patients$AMX)
# Or susceptible isolates
count_S(septic_patients$amox)
count_SI(septic_patients$amox)
count_S(septic_patients$AMX)
count_SI(septic_patients$AMX)
# Count all available isolates
count_all(septic_patients$amox)
n_rsi(septic_patients$amox)
count_all(septic_patients$AMX)
n_rsi(septic_patients$AMX)
# Since n_rsi counts available isolates, you can
# calculate back to count e.g. non-susceptible isolates.
# This results in the same:
count_IR(septic_patients$amox)
portion_IR(septic_patients$amox) * n_rsi(septic_patients$amox)
count_IR(septic_patients$AMX)
portion_IR(septic_patients$AMX) * n_rsi(septic_patients$AMX)
library(dplyr)
septic_patients \%>\%
group_by(hospital_id) \%>\%
summarise(R = count_R(cipr),
I = count_I(cipr),
S = count_S(cipr),
n1 = count_all(cipr), # the actual total; sum of all three
n2 = n_rsi(cipr), # same - analogous to n_distinct
summarise(R = count_R(CIP),
I = count_I(CIP),
S = count_S(CIP),
n1 = count_all(CIP), # the actual total; sum of all three
n2 = n_rsi(CIP), # same - analogous to n_distinct
total = n()) # NOT the number of tested isolates!
# 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_S` calculates percentages right away instead.
count_S(septic_patients$amcl) # S = 1342 (71.4\%)
count_all(septic_patients$amcl) # n = 1879
count_S(septic_patients$AMC) # S = 1342 (71.4\%)
count_all(septic_patients$AMC) # n = 1879
count_S(septic_patients$gent) # S = 1372 (74.0\%)
count_all(septic_patients$gent) # n = 1855
count_S(septic_patients$GEN) # S = 1372 (74.0\%)
count_all(septic_patients$GEN) # n = 1855
with(septic_patients,
count_S(amcl, gent)) # S = 1660 (92.3\%)
count_S(AMC, GEN)) # S = 1660 (92.3\%)
with(septic_patients, # n = 1798
n_rsi(amcl, gent))
n_rsi(AMC, GEN))
# Get portions S/I/R immediately of all rsi columns
septic_patients \%>\%
select(amox, cipr) \%>\%
select(AMX, CIP) \%>\%
count_df(translate = FALSE)
# It also supports grouping variables
septic_patients \%>\%
select(hospital_id, amox, cipr) \%>\%
select(hospital_id, AMX, CIP) \%>\%
group_by(hospital_id) \%>\%
count_df(translate = FALSE)