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(v1.4.0.9041) updates based on review

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dr. M.S. (Matthijs) Berends
2020-12-17 16:22:25 +01:00
parent 1faa816090
commit 81af41da3a
74 changed files with 710 additions and 627 deletions
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R/first_isolate.R
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@ -31,7 +31,7 @@
#' @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()].
#' @param col_testcode column name of the test codes. Use `col_testcode = NULL` to **not** exclude certain test codes (like test codes for screening). In that case `testcodes_exclude` will be ignored.
#' @param col_testcode column name of the test codes. Use `col_testcode = NULL` to **not** exclude certain test codes (such as test codes for screening). In that case `testcodes_exclude` will be ignored.
#' @param col_specimen column name of the specimen type or group
#' @param col_icu column name of the logicals (`TRUE`/`FALSE`) whether a ward or department is an Intensive Care Unit (ICU)
#' @param col_keyantibiotics column name of the key antibiotics to determine first *weighted* isolates, see [key_antibiotics()]. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use `col_keyantibiotics = FALSE` to prevent this.