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(v1.0.0.9007) small doc fix

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dr. M.S. (Matthijs) Berends
2020-02-22 17:03:47 +01:00
parent 0595af2801
commit 0d5e78b2cf
21 changed files with 48 additions and 60 deletions
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2
R/data.R
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@ -163,7 +163,7 @@ catalogue_of_life <- list(
#' Data set with unclean data
#'
#' A data set containing 3,000 microbial isolates that are not cleaned up and consequently not really for AMR analysis. This data set can be used for practice.
#' A data set containing 3,000 microbial isolates that are not cleaned up and consequently not ready for AMR analysis. This data set can be used for practice.
#' @format A [`data.frame`] with 3,000 observations and 8 variables:
#' - `patient_id`\cr ID of the patient
#' - `date`\cr date of receipt at the laboratory

2
R/filter_ab_class.R
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@ -21,7 +21,7 @@
#' Filter isolates on result in antibiotic class
#'
#' Filter isolates on results in specific antibiotic variables based on their class (ATC groups). This makes it easy to get a list of isolates that were tested for e.g. any aminoglycoside.
#' Filter isolates on results in specific antibiotic variables based on their antibiotic class. This makes it easy to filter on isolates that were tested for e.g. any aminoglycoside.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a data set
#' @param ab_class an antimicrobial class, like `"carbapenems"`, as can be found in [`antibiotics$group`][antibiotics]

1
R/first_isolate.R
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@ -22,6 +22,7 @@
#' Determine first (weighted) isolates
#'
#' Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.
#' @inheritSection lifecycle Stable lifecycle
#' @param x a [`data.frame`] containing isolates.
#' @param col_date column name of the result date (or date that is was received on the lab), defaults to the first column of 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)