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AMR
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small text fixes

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dr. M.S. (Matthijs) Berends 2018-12-14 07:48:12 +01:00
parent 81af7be36e
commit 7e5fe75a17
8 changed files with 13 additions and 16 deletions
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2
R/count.R
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@ -43,7 +43,7 @@
#' count_R(septic_patients$amox) #' count_R(septic_patients$amox)
#' count_IR(septic_patients$amox) #' count_IR(septic_patients$amox)
#' #'
#' # Or susceptibile isolates #' # Or susceptible isolates
#' count_S(septic_patients$amox) #' count_S(septic_patients$amox)
#' count_SI(septic_patients$amox) #' count_SI(septic_patients$amox)
#' #'

4
R/data.R
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@ -194,9 +194,9 @@
#' \item{\code{ward_clinical}}{logical to determine if ward is a regular clinical ward} #' \item{\code{ward_clinical}}{logical to determine if ward is a regular clinical ward}
#' \item{\code{ward_outpatient}}{logical to determine if ward is an outpatient clinic} #' \item{\code{ward_outpatient}}{logical to determine if ward is an outpatient clinic}
#' \item{\code{age}}{age of the patient} #' \item{\code{age}}{age of the patient}
#' \item{\code{sex}}{sex of the patient} #' \item{\code{gender}}{gender of the patient}
#' \item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information} #' \item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
#' \item{\code{mo}}{ID of microorganism, see \code{\link{microorganisms}}} #' \item{\code{mo}}{ID of microorganism created with \code{\link{as.mo}}, see also \code{\link{microorganisms}}}
#' \item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}} #' \item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}}
#' } #' }
#' @examples #' @examples

4
R/first_isolate.R
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@ -205,10 +205,6 @@ first_isolate <- function(tbl,
stop('Please check tbl for existance.') stop('Please check tbl for existance.')
} }
if (is.na(column)) {
column <- NULL
}
if (!is.null(column)) { if (!is.null(column)) {
if (!(column %in% colnames(tblname))) { if (!(column %in% colnames(tblname))) {
stop('Column `', column, '` not found.') stop('Column `', column, '` not found.')

2
R/portion.R
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@ -52,7 +52,7 @@
#' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}. #' @source \strong{M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition}, 2014, \emph{Clinical and Laboratory Standards Institute (CLSI)}. \url{https://clsi.org/standards/products/microbiology/documents/m39/}.
#' #'
#' Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html} #' Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html}
#' @seealso \code{\link[AMR]{count}_*} to count resistant and susceptibile isolates. #' @seealso \code{\link[AMR]{count}_*} to count resistant and susceptible isolates.
#' @keywords resistance susceptibility rsi_df rsi antibiotics isolate isolates #' @keywords resistance susceptibility rsi_df rsi antibiotics isolate isolates
#' @return Double or, when \code{as_percent = TRUE}, a character. #' @return Double or, when \code{as_percent = TRUE}, a character.
#' @rdname portion #' @rdname portion

2
man/count.Rd
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@ -66,7 +66,7 @@ These functions are meant to count isolates. Use the \code{\link{portion}_*} fun
count_R(septic_patients$amox) count_R(septic_patients$amox)
count_IR(septic_patients$amox) count_IR(septic_patients$amox)
# Or susceptibile isolates # Or susceptible isolates
count_S(septic_patients$amox) count_S(septic_patients$amox)
count_SI(septic_patients$amox) count_SI(septic_patients$amox)

2
man/portion.Rd
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@ -155,7 +155,7 @@ my_table \%>\%
} }
} }
\seealso{ \seealso{
\code{\link[AMR]{count}_*} to count resistant and susceptibile isolates. \code{\link[AMR]{count}_*} to count resistant and susceptible isolates.
} }
\keyword{antibiotics} \keyword{antibiotics}
\keyword{isolate} \keyword{isolate}

4
man/septic_patients.Rd
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@ -12,9 +12,9 @@
\item{\code{ward_clinical}}{logical to determine if ward is a regular clinical ward} \item{\code{ward_clinical}}{logical to determine if ward is a regular clinical ward}
\item{\code{ward_outpatient}}{logical to determine if ward is an outpatient clinic} \item{\code{ward_outpatient}}{logical to determine if ward is an outpatient clinic}
\item{\code{age}}{age of the patient} \item{\code{age}}{age of the patient}
\item{\code{sex}}{sex of the patient} \item{\code{gender}}{gender of the patient}
\item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information} \item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
\item{\code{mo}}{ID of microorganism, see \code{\link{microorganisms}}} \item{\code{mo}}{ID of microorganism created with \code{\link{as.mo}}, see also \code{\link{microorganisms}}}
\item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}} \item{\code{peni:rifa}}{40 different antibiotics with class \code{rsi} (see \code{\link{as.rsi}}); these column names occur in \code{\link{antibiotics}} data set and can be translated with \code{\link{abname}}}
}} }}
\usage{ \usage{

9
tests/testthat/test-first_isolate.R
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@ -17,10 +17,11 @@ test_that("first isolates work", {
suppressWarnings( suppressWarnings(
sum( sum(
first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)), first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
col_date = "date", # let syntax determine these automatically:
col_patient_id = "patient_id", # col_date = "date",
col_mo = "mo", # col_patient_id = "patient_id",
col_keyantibiotics = "keyab", # col_mo = "mo",
# col_keyantibiotics = "keyab",
type = "keyantibiotics", type = "keyantibiotics",
info = TRUE), info = TRUE),
na.rm = TRUE)), na.rm = TRUE)),