merge_strip: Merge Concept Attributes into a Strip

Description Usage Arguments Value See Also

View source: R/format.R

Description

All the OMOP Vocabulary Concept Table fields other than the date fields are "merged"into a single string, called a "Strip". If the Strip output is '<NA>' while the input concept id is not, a flagMergeStrip object is returned in the Global Environment.

Usage

1
merge_strip(data, into, ..., suffix = NULL, prefix = NULL)

Arguments

data

dataframe with the following required fields from the output

into

name of the column that the new combined string will be in

...

columns other than concept_id that will be removed in tidyr unite but should be preserved in addition to be merged.

suffix

if the omop concept element column names are different from the standard by a suffix, include it so it can point to the correct set of columns

prefix

if the omop concept element column names are prefixed, include it so it can point to the correct set of columns

Value

A tibble with all blank and "NA" normalized to '<NA>' with 1. If present, 'valid_start_date' and 'valid_end_date' fields are permanently removed, 2. 8 out of the 10 remaining Concept Table fields (concept_id, concept_name, domain_id, vocabulary_id, concept_class_id, standard_concept, concept_code, invalid_reason) are merged into a single column with the provided column name, 3. the concept_id column is renamed to the format of the provided merged column name: into_concept_id. The remaining of the 7 Concept Table fields may also be preserved outside of the merge if provided. All other columns present in the input data are returned along with the transformations described.

See Also

tidyeval-compat,mutate_all,vars,reexports,select,filter_all,all_vars,bind unite as_tibble normalize_all_to_na

Other concept format functions: filter_at_all_strip(), filter_at_any_strip(), filter_strip(), get_strip(), label_to_strip(), merge_label(), unbox_label(), unbox_strip(), unmerge_label(), unmerge_strip()


patelm9/chariot documentation built on Feb. 19, 2022, 11:29 a.m.