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fix clipboard on linux

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dr. M.S. (Matthijs) Berends
2018-04-02 11:11:21 +02:00
parent abcb4accbd
commit c182a9673d
12 changed files with 181 additions and 176 deletions
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24
man/first_isolate.Rd
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@ -14,17 +14,17 @@ first_isolate(tbl, col_date, col_patient_id, col_bactid = NA,
\arguments{
\item{tbl}{a \code{data.frame} containing isolates.}
\item{col_date}{column name of the result date (or date that is was received on the lab), supports tidyverse-like quotation}
\item{col_date}{column name of the result date (or date that is was received on the lab)}
\item{col_patient_id}{column name of the unique IDs of the patients, supports tidyverse-like quotation}
\item{col_patient_id}{column name of the unique IDs of the patients}
\item{col_bactid}{column name of the unique IDs of the microorganisms (should occur in the \code{\link{microorganisms}} dataset), supports tidyverse-like quotation}
\item{col_bactid}{column name of the unique IDs of the microorganisms (should occur in the \code{\link{microorganisms}} dataset)}
\item{col_testcode}{column name of the test codes. Use \code{col_testcode = NA} to \strong{not} exclude certain test codes (like test codes for screening). In that case \code{testcodes_exclude} will be ignored. Supports tidyverse-like quotation.}
\item{col_specimen}{column name of the specimen type or group, supports tidyverse-like quotation}
\item{col_specimen}{column name of the specimen type or group}
\item{col_icu}{column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU), supports tidyverse-like quotation}
\item{col_icu}{column name of the logicals (\code{TRUE}/\code{FALSE}) whether a ward or department is an Intensive Care Unit (ICU)}
\item{col_keyantibiotics}{column name of the key antibiotics to determine first \emph{weighted} isolates, see \code{\link{key_antibiotics}}. Supports tidyverse-like quotation.}
@ -46,9 +46,9 @@ first_isolate(tbl, col_date, col_patient_id, col_bactid = NA,
\item{info}{print progress}
\item{col_genus}{(deprecated, use \code{col_bactid} instead) column name of the genus of the microorganisms, supports tidyverse-like quotation}
\item{col_genus}{(deprecated, use \code{col_bactid} instead) column name of the genus of the microorganisms}
\item{col_species}{(deprecated, use \code{col_bactid} instead) column name of the species of the microorganisms, supports tidyverse-like quotation}
\item{col_species}{(deprecated, use \code{col_bactid} instead) column name of the species of the microorganisms}
}
\value{
A vector to add to table, see Examples.
@ -73,12 +73,10 @@ my_patients <- septic_patients
library(dplyr)
my_patients$first_isolate <- my_patients \%>\%
left_join_microorganisms() \%>\%
first_isolate(col_date = date,
col_patient_id = patient_id,
col_genus = genus,
col_species = species)
first_isolate(col_date = "date",
col_patient_id = "patient_id",
col_bactid = "bactid")
\dontrun{
# set key antibiotics to a new variable