create_param | R Documentation |
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 named 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$N
, storing dates of infections for
each case.
kappa
: A list of length size
. Each item of the list is
an integer vector of length data$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.
a
: A numeric vector of length size
, storing values of
the first spatial parameter (population).
b
: A numeric vector of length size
, storing values of
the second spatial parameter (distance).
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.
kappa
: An integer vector of length data$N
, storing the
number of generations before the last sampled ancestor for each case.
pi
: The value of the reporting probability.
a
: The value of the first spatial parameter (population).
b
: The value of the second spatial parameter (distance).
log_s_dens
:The spatial likelihood matrix, calculated at each step
from a and b if move_a == TRUE or move_b == TRUE.
Initial version by Thibaut Jombart, rewritten by Alexis Robert (alexis.robert@lshtm.ac.uk)
## load data
data("toy_outbreak_short")
dt_cases <- toy_outbreak_short$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)
## 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)
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