create_param.RdThis 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$N, storing the
number of generations before the last sampled ancestor for each case.
pi: The value of the reporting probability.
eps: The value of the contact reporting coverage.
lambda: The value of the non-infectious contact rate.
Thibaut Jombart (thibautjombart@gmail.com)
## load data x <- fake_outbreak data <- outbreaker_data(dates = x$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)