calc_adjusted_incidence: Compute crude & adjusted incidence from a count data

In cturbelin/ifnBase: InfluenzaNet Data Analysis Base

Compute crude & adjusted incidence from a count data

Description

This function is shared by all incidence computation methods, once active participants & syndrome counts are provided

Usage

calc_adjusted_incidence(count.week, design, syndromes, output)

Arguments

count.week	data.frame(), count for a week. Count of active participants is in "active" column
design	design structure (defining strata and reference data like population in each strata)
syndromes	char() list of column names for each syndrome count
output	char() list of requested output "inc"=global incidence, "zlow"=lower geo level incidence, "age" by age incidence,

Details

Ouput columns are ([syndrome] is the column with logical value for presence of one syndrome in the weekly data, for example "ili"): - active : count of active participants - [syndrome] : count for this syndrome (or variable) - [syndrome].crude : crude incidence (without adjustment, count/active participant ratio) - [syndrome].adj : Adjusted incidence (taking into account of stratification design) - [syndrome].crude.(upper|lower) : upper & lower bound of CI95 for crude incidence (Exact poisson CI) - [syndrome].adj.(upper|lower) : upper & lower boud of CI95 for ajusted incidence (DKES method)

cturbelin/ifnBase documentation built on Nov. 5, 2023, 12:54 p.m.