calc_adjusted_incidence: Compute crude & adjusted incidence from a count data

Description Usage Arguments Details

View source: R/incidence_design.R

Description

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

Usage

1
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 Jan. 10, 2020, 1:44 a.m.