incidence.from.DS1: Compute incidence from data stream 1

In annecori/mRIIDSprocessData: Epidemiological forcasting using real-time data

Description

This function serves as a wrapper around the cleaning and processing of incidence data. The functions for these are available in ...

Usage

incidence.from.DS1(case_count, species, disease, case_type = c("scc", "sc",
  "cc", "scd", "sd", "cd", "ALL"), location, merge_rule = c("median"))

Arguments

case_count	dataframe containing data stream 1 to be processed
species	string giving species in which disease incidence will be extracted
disease	string specifying disease of interest
case_type	string specifying column name from which incidence is extracted; one of "scc" (suspected and confirmed cases), "sc" (suspected cases), "cc" (confirmed cases), "scD" (suspected and confirmed deaths), "sd" (suspected deaths), or "cd" (confirmed deaths).
location	string specifying location for which incidence will be computed
merge_rule	string to specify how merging should be made when duplicated entries exist. At the moment only "median" is supported.

Details

XXX

Value

a dataframe containing incidence and cumulative incidence obtained from merged_dat.

Author(s)

Pierre Nouvellet, Anne Cori and Sangeeta Bhatia

Examples

# to be written

annecori/mRIIDSprocessData documentation built on May 29, 2019, 1:16 p.m.