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new class bactid

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dr. M.S. (Matthijs) Berends
2018-07-23 14:14:03 +02:00
parent 40de1b4ac2
commit 8421638b60
21 changed files with 408 additions and 251 deletions
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man/first_isolate.Rd
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@ -1,5 +1,5 @@
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/first_isolates.R
% Please edit documentation in R/first_isolate.R
\name{first_isolate}
\alias{first_isolate}
\title{Determine first (weighted) isolates}
@ -21,7 +21,7 @@ first_isolate(tbl, col_date, col_patient_id, col_bactid = NA,
\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). Get your bactid's with the function \code{\link{guess_bactid}}, that takes microorganism names as input.}
\item{col_bactid}{column name of the unique IDs of the microorganisms: \code{bactid}'s. If this column has another class than \code{"bactid"}, values will be coerced using \code{\link{as.bactid}}.}
\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.}