ann_tab_long: Create long annual tables from line listing data

In PublicHealthEngland/hcaidcs: R functions for the mandatory surveillance of bacteraemia and C. difficile infection

Create long annual tables from line listing data

Description

From FY 2018/19, annual tables will be moving to a long format rather than a wide format. This function takes line-listing data and aggregates by organisation and time period, producing counts of cases by a given metric (apportioning or prior healthcare exposure).

Usage

ann_tab_long(dat, collection_var, org_var, metric_var, period_var)

Arguments

dat	A dataframe containing line-listing data
collection_var	A string giving the data collection
org_var	The variable giving the organisation code
metric_var	Column in dat giving column for the metric
period_var	Column giving the period by which counts should be aggregated

Details

The data are expanded to cover time periods in the data, but there may well be organisations that are not in the line-listing data that will be merged in later to make a complete table.

In addition, PHEC and organisation names will need to be merged in, as will denominator data, and rates will need to be calculated.

Value

A dataframe with counts of cases in long format, by organisation and time period

Examples

library(dplyr)
data(line_listing)
line_listing$fy_long <- fy_long(line_listing$specimen_date)

line_listing %>%
  filter(collection == "C. difficile") %>%
  ann_tab_long(dat = ., collection_var = collection,
    org_var = reporting_organisation_code,
    metric_var = prior_hc, period_var = fy_long)

PublicHealthEngland/hcaidcs documentation built on Jan. 19, 2024, 8:38 a.m.