manipulateSqlPull: This function performs the manipulation of the sql extract...

In OHDSI/Aphrodite: Automated PHenotype Routine for Observational Definition Identification Training and Evaluation (APHRODITE) - Phenotype building tool using Fuzzy labels

Description

This function performs the manipulation of the sql extract data; should be generic for any of the feature types

Usage

manipulateSqlPull(tmp_fv, flags, timeDiff)

Arguments

tmp_fv	Pull from sql query. Should have a column for date and concept_id
flags	Flags set in settings - specifies which normalization is needed
timeDiff	Value to use for normalization

Details

This is just a helper function that reduces the repeats of code for the manipulation of the sql extract data, so that it is put in the desired format for compiling all patient features together. This function: gets the counts of codes on a given visit (so multiple codes/terms/drugs/etc are not all counted); normalizes based on the normalization setting; returns a data frame with counts of codes

Value

An object containing the re-formatted patient data: ptID x (num concept IDs) - filled with counts, deduplicated by visit

Examples

## Not run: 

 test1 <- manipulateSqlPull(tmp_fv, flags, timeDiff)


## End(Not run)

OHDSI/Aphrodite documentation built on Sept. 18, 2020, 10:26 p.m.