followup_priorities: Compute the followup priorities for a list of contacts

In ffinger/followup: Evidence based prioritisation of contacts to follow-up during infectious disease outbreaks

Description

Outputs the probability that the symptoms onset of a contact was between the last follow up (day of last follow up not included in interval) and the analysis date, which defaults to day before current system date and is included in interval.

Usage

followup_priorities(contact_list, exposure, exposure_end = NULL,
  rate_infectious_contact = NULL, last_followup = NULL,
  p_disease = 1, incubation_period = NULL,
  date_analysis = Sys.Date(), sort = TRUE)

Arguments

contact_list	A data.frame with one row per contact, containing at least a column with possible dates of exposure.
exposure	The name of the column of contact_list containing the dates of exposure (variable name or in quotes). Can be a list column containing vectors with several possible exposure dates per contact.
exposure_end	The name of a column containing dates representing the end of the exposure period. This is NULL by default, indicating all exposures are in the exposure column.
rate_infectious_contact	a vector containing rates of infectious contact corresponding to each exposure date in exposure, or between exposure and exposure_end. same length as exposure. Defaults to rep(1, length(exposure)).
last_followup	The name of the column of contact_list containing the last follow up date for each contact (variable name or in quotes). Should contain NA if unknown or contact has never been followed.
incubation_period	The incubation period distribution. Can be a distcrete distribution, an empirical incubation period returned by epitrix::empirical_incubation_dist() (of type data.frame) or an atomic vector whose elements 1:n correspond to the probability of the incubation period being 0:(n-1).
date_analysis	the date on which the prioritization should be done. The probability of symptoms onset is computed until the end of the previous day. Defaults to the system date (i.e. today).
sort	If TRUE (default) the result is sorted by followup priority.

Value

A data.frame containing all columns in contact_list and the following additional columns:

• rate_onset the overall rate of disease onset by date_analysis

• p_onset the overall probability of disease onset by date_analysis

• followup_priority, an index ranging from 1 for the highest priority to the number of patients

ffinger/followup documentation built on Jan. 28, 2021, 3:20 a.m.