outbreaker_data {outbreaker2}

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

Acceptables arguments for ... are:

dates

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. If the vector is named, the vector names will be used for matching cases to contact tracing data and labelled DNA sequences.

dna

the DNA sequences in DNAbin format (see read.dna in the ape package); this can be imported from a fasta file (extension .fa, .fas, or .fasta) using adegenet's function fasta2DNAbin.

ctd

the contact tracing data provided as a matrix/dataframe of two columns, indicating a reported contact between the two individuals whose ids are provided in a given row of the data, or an epicontacts object. In the case of the latter, linelist IDs will be used for matching dates and DNA sequences

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 colonization time, i_e. time interval during which the pathogen can be sampled from the patient.

Author(s)

Thibaut Jombart ([e-mail])

Examples

x <- fake_outbreak
outbreaker_data(dates = x$sample, dna = x$dna, w_dens = x$w)