`create_param.Rd`

This function creates initial outputs and parameter states for outbreaker.

create_param(data = outbreaker_data(), config = create_config())

data | A list of data items as returned by |
---|---|

config | A list of settings as returned by |

A list containing two components `$store`

and
`$current`

. `store`

is a list with the class
`outbreaker_store`

, used for storing 'saved' states of the
MCMC. `current`

is a list with the class `outbreaker_param`

, used
for storing 'current' states of the MCMC.

`outbreaker_store`

class content:

`size`

: The length of the list, corresponding to the number of samples saved from the MCMC.`step`

: A vector of integers of length`size`

, storing the steps of the MCMC corresponding to the saved samples.`post`

: A numeric vector of length`size`

, storing log-posterior values.`like`

: A numeric vector of length`size`

, storing log-likelihood values.`prior`

: A numeric vector of length`size`

, storing log-prior values.`alpha`

: A list of length`size`

. Each item of the list is an integer vector of length`data$N`

, storing indices (from 1 to N) of infectors for each case.`t_inf`

: A list of length`size`

. Each item of the list is an integer vector of length`data$N`

, storing dates of infections for each case.`mu`

: A numeric vector of length`size`

, storing values of the mutation rate.`kappa`

: A list of length`size`

. Each item of the list is an integer vector of length`data$N`

, storing the number of generations before the last sampled ancestor for each case.`pi`

: A numeric vector of length`size`

, storing values of the reporting probability.`eps`

: A numeric vector of length`size`

, storing values of the contact reporting coverage.`lambda`

: A numeric vector of length`size`

, storing values of the non-infectious contact rate.`counter`

: A counter used to keep track of the current iteration of the MCMC (used internally).

`outbreaker_param`

class content:

`alpha`

: An integer vector of length`data$N`

, storing indices (from 1 to N) of infectors for each case.`t_inf`

: An integer vector of length`data$N`

, storing dates of infections for each case.`mu`

: The value of the mutation rate.`kappa`

: An integer vector of length`data$N`

, storing the number of generations before the last sampled ancestor for each case.`pi`

: The value of the reporting probability.`eps`

: The value of the contact reporting coverage.`lambda`

: The value of the non-infectious contact rate.

## load data x <- fake_outbreak data <- outbreaker_data(dates = x$sample, dna = x$dna, w_dens = x$w) ## modify config settings config <- create_config(move_alpha = FALSE, n_iter = 2e5, sample_every = 1000) ## create param object param <- create_param(data = data, config = config)