calc_count_by_site_inst: Calculate pathogen count by site and instrument version

In MartinHoldrege/turnr: Normalization of Test Utilization Rate

Description

Calculates the number of each pathogen found on a given date for each site and instrument version (also for all instrument versions combined). To reduce the size of the output, pathogens are not listed on dates they were not detected.

Usage

calc_count_by_site_inst(df, target_PouchTitle = "Respiratory_Panel")

Arguments

df	Data frame that has been processed by pre_process() and has at least "RunDataID", "TargetName", "PouchTitle" "date", "InstrumentVersion", "SiteID" columns
target_PouchTitle	Name of the PouchTitle of interest

Value

Dataframe with columns "SiteID", "date", "daily_count" (number of tests positive for that pathogen that day), "TargetName" (name of pathogen, and "InstrumentVersion" (either the name of the instrument, or 'all', for all instrument versions combined)

Note

This function is slow and can take at least several minutes to run when large dataframe is used.

Examples

df <- pre_process(rp_raw)
calc_count_by_site_inst(df)

MartinHoldrege/turnr documentation built on May 16, 2020, 10:39 a.m.