P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 20:02:04 +02:00
Code Releases Activity

(v1.4.0.9050) ab selectors base R

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2020-12-27 20:32:40 +01:00
parent 175e33abba
commit afc325c314
33 changed files with 88 additions and 65 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
R/first_isolate.R
View File

@ -27,7 +27,7 @@
#'
#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type. To determine patient episodes not necessarily based on microorganisms, use [is_new_episode()] that also supports grouping with the `dplyr` package.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a [data.frame] containing isolates. Can be omitted when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
#' @param x a [data.frame] containing isolates. Can be left blank when used inside `dplyr` verbs, such as [`filter()`][dplyr::filter()], [`mutate()`][dplyr::mutate()] and [`summarise()`][dplyr::summarise()].
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column with a date class
#' @param col_patient_id column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)
#' @param col_mo column name of the IDs of the microorganisms (see [as.mo()]), defaults to the first column of class [`mo`]. Values will be coerced using [as.mo()].
@ -46,7 +46,7 @@
#' @param include_unknown logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code `"UNKNOWN"`, which defaults to `FALSE`. For WHONET users, this means that all records with organism code `"con"` (*contamination*) will be excluded at default. Isolates with a microbial ID of `NA` will always be excluded as first isolate.
#' @param ... arguments passed on to [first_isolate()] when using [filter_first_isolate()], or arguments passed on to [key_antibiotics()] when using [filter_first_weighted_isolate()]
#' @details
#' These functions are context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the `x` argument can be omitted, please see *Examples*.
#' These functions are context-aware when used inside `dplyr` verbs, such as `filter()`, `mutate()` and `summarise()`. This means that then the `x` argument can be left blank, please see *Examples*.
#'
#' The [first_isolate()] function is a wrapper around the [is_new_episode()] function, but more efficient for data sets containing microorganism codes or names.
#'