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small text fixes
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@ -43,7 +43,7 @@
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#' count_R(septic_patients$amox)
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#' count_IR(septic_patients$amox)
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#'
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#' # Or susceptibile isolates
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#' # Or susceptible isolates
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#' count_S(septic_patients$amox)
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#' count_SI(septic_patients$amox)
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#'
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4
R/data.R
4
R/data.R
@ -194,9 +194,9 @@
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#' \item{\code{ward_clinical}}{logical to determine if ward is a regular clinical ward}
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#' \item{\code{ward_outpatient}}{logical to determine if ward is an outpatient clinic}
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#' \item{\code{age}}{age of the patient}
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#' \item{\code{sex}}{sex of the patient}
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#' \item{\code{gender}}{gender of the patient}
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#' \item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
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#' \item{\code{mo}}{ID of microorganism, see \code{\link{microorganisms}}}
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#' \item{\code{mo}}{ID of microorganism created with \code{\link{as.mo}}, see also \code{\link{microorganisms}}}
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#' \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}}}
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#' }
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#' @examples
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@ -205,10 +205,6 @@ first_isolate <- function(tbl,
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stop('Please check tbl for existance.')
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}
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if (is.na(column)) {
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column <- NULL
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}
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if (!is.null(column)) {
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if (!(column %in% colnames(tblname))) {
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stop('Column `', column, '` not found.')
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@ -52,7 +52,7 @@
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#' @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/}.
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#'
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#' Wickham H. \strong{Tidy Data.} The Journal of Statistical Software, vol. 59, 2014. \url{http://vita.had.co.nz/papers/tidy-data.html}
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#' @seealso \code{\link[AMR]{count}_*} to count resistant and susceptibile isolates.
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#' @seealso \code{\link[AMR]{count}_*} to count resistant and susceptible isolates.
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#' @keywords resistance susceptibility rsi_df rsi antibiotics isolate isolates
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#' @return Double or, when \code{as_percent = TRUE}, a character.
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#' @rdname portion
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@ -66,7 +66,7 @@ These functions are meant to count isolates. Use the \code{\link{portion}_*} fun
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count_R(septic_patients$amox)
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count_IR(septic_patients$amox)
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# Or susceptibile isolates
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# Or susceptible isolates
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count_S(septic_patients$amox)
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count_SI(septic_patients$amox)
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@ -155,7 +155,7 @@ my_table \%>\%
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}
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}
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\seealso{
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\code{\link[AMR]{count}_*} to count resistant and susceptibile isolates.
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\code{\link[AMR]{count}_*} to count resistant and susceptible isolates.
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}
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\keyword{antibiotics}
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\keyword{isolate}
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@ -12,9 +12,9 @@
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\item{\code{ward_clinical}}{logical to determine if ward is a regular clinical ward}
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\item{\code{ward_outpatient}}{logical to determine if ward is an outpatient clinic}
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\item{\code{age}}{age of the patient}
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\item{\code{sex}}{sex of the patient}
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\item{\code{gender}}{gender of the patient}
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\item{\code{patient_id}}{ID of the patient, first 10 characters of an SHA hash containing irretrievable information}
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\item{\code{mo}}{ID of microorganism, see \code{\link{microorganisms}}}
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\item{\code{mo}}{ID of microorganism created with \code{\link{as.mo}}, see also \code{\link{microorganisms}}}
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\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}}}
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}}
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\usage{
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@ -17,10 +17,11 @@ test_that("first isolates work", {
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suppressWarnings(
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sum(
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first_isolate(tbl = septic_patients %>% mutate(keyab = key_antibiotics(.)),
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col_date = "date",
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col_patient_id = "patient_id",
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col_mo = "mo",
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col_keyantibiotics = "keyab",
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# let syntax determine these automatically:
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# col_date = "date",
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# col_patient_id = "patient_id",
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# col_mo = "mo",
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# col_keyantibiotics = "keyab",
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type = "keyantibiotics",
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info = TRUE),
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na.rm = TRUE)),
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