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count_all and some fixes

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dr. M.S. (Matthijs) Berends
2018-10-12 16:35:18 +02:00
parent e7d937d36e
commit 5b5b95a47b
22 changed files with 232 additions and 246 deletions
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42
man/count.Rd
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@ -7,6 +7,8 @@
\alias{count_I}
\alias{count_SI}
\alias{count_S}
\alias{count_all}
\alias{n_rsi}
\alias{count_df}
\title{Count isolates}
\source{
@ -23,11 +25,15 @@ count_SI(...)
count_S(...)
count_all(...)
n_rsi(...)
count_df(data, translate_ab = getOption("get_antibiotic_names",
"official"))
}
\arguments{
\item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed. Use multiple columns to calculate (the lack of) co-resistance: the probability where one of two drugs have a resistant or susceptible result. See Examples.}
\item{...}{one or more vectors (or columns) with antibiotic interpretations. They will be transformed internally with \code{\link{as.rsi}} if needed.}
\item{data}{a \code{data.frame} containing columns with class \code{rsi} (see \code{\link{as.rsi}})}
@ -42,10 +48,10 @@ These functions can be used to count resistant/susceptible microbial isolates. A
\code{count_R} and \code{count_IR} can be used to count resistant isolates, \code{count_S} and \code{count_SI} can be used to count susceptible isolates.\cr
}
\details{
\strong{Remember that you should filter your table to let it contain only first isolates!} Use \code{\link{first_isolate}} to determine them in your data set.
These functions are meant to count isolates. Use the \code{\link{portion}_*} functions to calculate microbial resistance.
\code{n_rsi} is an alias of \code{count_all}. They can be used to count all available isolates, i.e. where all input antibiotics have an available result (S, I or R). Their use is equal to \code{\link{n_distinct}}. Their function is equal to \code{count_S(...) + count_IR(...)}.
\code{count_df} takes any variable from \code{data} that has an \code{"rsi"} class (created with \code{\link{as.rsi}}) and counts the amounts of R, I and S. The resulting \emph{tidy data} (see Source) \code{data.frame} will have three rows (S/I/R) and a column for each variable with class \code{"rsi"}.
}
\examples{
@ -60,6 +66,10 @@ count_IR(septic_patients$amox)
count_S(septic_patients$amox)
count_SI(septic_patients$amox)
# Count all available isolates
count_all(septic_patients$amox)
n_rsi(septic_patients$amox)
# Since n_rsi counts available isolates, you can
# calculate back to count e.g. non-susceptible isolates.
# This results in the same:
@ -69,24 +79,25 @@ portion_IR(septic_patients$amox) * n_rsi(septic_patients$amox)
library(dplyr)
septic_patients \%>\%
group_by(hospital_id) \%>\%
summarise(R = count_R(cipr),
I = count_I(cipr),
S = count_S(cipr),
n = n_rsi(cipr), # the actual total; sum of all three
total = n()) # NOT the amount of tested isolates!
summarise(R = count_R(cipr),
I = count_I(cipr),
S = count_S(cipr),
n1 = count_all(cipr), # the actual total; sum of all three
n2 = n_rsi(cipr), # same - analogous to n_distinct
total = n()) # NOT the amount of tested isolates!
# Count co-resistance between amoxicillin/clav acid and gentamicin,
# so we can see that combination therapy does a lot more than mono therapy.
# Please mind that `portion_S` calculates percentages right away instead.
count_S(septic_patients$amcl) # S = 1056 (67.3\%)
n_rsi(septic_patients$amcl) # n = 1570
count_S(septic_patients$amcl) # S = 1057 (67.1\%)
count_all(septic_patients$amcl) # n = 1576
count_S(septic_patients$gent) # S = 1363 (74.0\%)
n_rsi(septic_patients$gent) # n = 1842
count_S(septic_patients$gent) # S = 1372 (74.0\%)
count_all(septic_patients$gent) # n = 1855
with(septic_patients,
count_S(amcl, gent)) # S = 1385 (92.1\%)
with(septic_patients, # n = 1504
count_S(amcl, gent)) # S = 1396 (92.0\%)
with(septic_patients, # n = 1517
n_rsi(amcl, gent))
# Get portions S/I/R immediately of all rsi columns
@ -102,8 +113,7 @@ septic_patients \%>\%
}
\seealso{
\code{\link{portion}_*} to calculate microbial resistance and susceptibility.\cr
\code{\link{n_rsi}} to count all cases where antimicrobial results are available.
\code{\link{portion}_*} to calculate microbial resistance and susceptibility.
}
\keyword{antibiotics}
\keyword{isolate}