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- For functions first_isolate, EUCAST_rules the antibiotic column names are case-insensitive

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- Functions `first_isolate`, `EUCAST_rules` and `rsi_predict` supports tidyverse-like evaluation of parameters (no need to quote columns them anymore)
- Functions `clipboard_import` and `clipboard_export` as helper functions to quickly copy and paste from/to software like Excel and SPSS
- Renamed dataset `bactlist` to `microorganisms`
This commit is contained in:
dr. M.S. (Matthijs) Berends
2018-03-23 14:46:02 +01:00
parent e1e19af625
commit 53464ff1c8
29 changed files with 693 additions and 373 deletions
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14
man/first_isolate.Rd
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@ -4,12 +4,12 @@
\alias{first_isolate}
\title{Determine first (weighted) isolates}
\usage{
first_isolate(tbl, col_date, col_patient_id, col_genus, col_species,
first_isolate(tbl, col_date, col_patient_id, col_bactid = NA,
col_testcode = NA, col_specimen = NA, col_icu = NA,
col_keyantibiotics = NA, episode_days = 365, testcodes_exclude = "",
icu_exclude = FALSE, filter_specimen = NA, output_logical = TRUE,
type = "keyantibiotics", ignore_I = TRUE, points_threshold = 2,
info = TRUE)
info = TRUE, col_genus = NA, col_species = NA)
}
\arguments{
\item{tbl}{a \code{data.frame} containing isolates.}
@ -18,9 +18,7 @@ first_isolate(tbl, col_date, col_patient_id, col_genus, col_species,
\item{col_patient_id}{column name of the unique IDs of the patients, supports tidyverse-like quotation}
\item{col_genus}{column name of the genus of the microorganisms, supports tidyverse-like quotation}
\item{col_species}{column name of the species of the microorganisms, supports tidyverse-like quotation}
\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_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.}
@ -47,6 +45,10 @@ first_isolate(tbl, col_date, col_patient_id, col_genus, col_species,
\item{points_threshold}{points until the comparison of key antibiotics will lead to inclusion of an isolate when \code{type = "points"}, see Details}
\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_species}{(deprecated, use \code{col_bactid} instead) column name of the species of the microorganisms, supports tidyverse-like quotation}
}
\value{
A vector to add to table, see Examples.
@ -71,7 +73,7 @@ my_patients <- septic_patients
library(dplyr)
my_patients$first_isolate <- my_patients \%>\%
left_join_bactlist() \%>\%
left_join_microorganisms() \%>\%
first_isolate(col_date = date,
col_patient_id = patient_id,
col_genus = genus,