outbreaker_data {o2geosocial}

Process input data for outbreaker

Description

This function performs various checks on input data given to outbreaker. It takes a list of named items as input, performs various checks, set defaults where arguments are missing, and return a correct list of data input. If no input is given, it returns the default settings.

Usage

outbreaker_data(..., data = list(...))

Arguments

...

a list of data items to be processed (see description)

data

optionally, an existing list of data item as returned by outbreaker_data.

Details

Acceptable arguments for ... are:

dates

a vector indicating the collection dates, provided either as integer numbers or in a usual date format such as Date or POSIXct format. By convention, zero will indicate the oldest date. Cases must be ordering by ascending onset date.

age_group

a vector indicating the age group of the cases, provided as integer numbers. The value of age group corresponds to the position of this age group in a_dens.

region

a vector indicating the region of the cases, provided as integer numbers or characters. If numeric, the value of the region corresponds to the position of the region in the distance matrix and the population vector. Otherwise, the value corresponds to the region and will be matched to the distance matrix and the population vector.

w_dens

a vector of numeric values indicating the generation time distribution, reflecting the infectious potential of a case t = 1, 2, ... time steps after infection. By convention, it is assumed that newly infected patients cannot see new infections on the same time step. If not standardized, this distribution is rescaled to sum to 1.

f_dens

similar to w_dens, except that this is the distribution of the incubation period, i_e. time interval between the reported onset date and the infection date.

a_dens

a matrix of numeric values indicating the contact between age groups, reflecting on the infectious potential of a case for a given age group.

genotype

a character vector showing the genotype in each case.

is_cluster

an integer vector indicating which group of cases each case belongs to.

s_dens

a matrix of numeric values indicating the initial value of the connectivity between region. Only needed if a and b are fixed in the model, otherwise NULL.

population

a double vector indicating the population in every region considered in the study.

distance

a double matrix indicating the distance between each region.

import

a logical vector indicating whether each case is an import (TRUE) or not (FALSE).

Value

A named list containing the value of each elements listed in the 'Details' section. This list describes the data that will be used by the function outbreaker().

Author(s)

Initial version by Thibaut Jombart, rewritten by Alexis Robert ([e-mail])

Examples

data("toy_outbreak_short")
dt_cases <- toy_outbreak_short$cases
dt_cases <- dt_cases[order(dt_cases$Date), ]
dt_regions <- toy_outbreak_short$dt_regions
all_dist <- geosphere::distGeo(matrix(c(rep(dt_regions$long, nrow(dt_regions)), 
                                        rep(dt_regions$lat, nrow(dt_regions))), 
                                      ncol = 2), 
                               matrix(c(rep(dt_regions$long, each = nrow(dt_regions)), 
                                        rep(dt_regions$lat, each = nrow(dt_regions))),
                                      ncol = 2))

dist_mat <- matrix(all_dist/1000, nrow = nrow(dt_regions))
pop_vect <- dt_regions$population
names(pop_vect) <- rownames(dist_mat) <- colnames(dist_mat) <- dt_regions$region
data <- outbreaker_data(dates = dt_cases$Date, age_group = dt_cases$age_group,
                        region = dt_cases$Cens_tract, population = pop_vect, 
                        distance = dist_mat)