priors {Bernadette}  R Documentation 
The functions described on this page are used to specify the priorrelated arguments of the modeling functions in the Bernadette package.
The default priors used in the Bernadette modeling functions
are intended to be weakly informative. For many applications the
defaults will perform well, but prudent use of more informative priors is
encouraged. Uniform prior distributions are possible (e.g. by setting
stan_igbm
's prior
argument to NULL
) but, unless
the data is very strong, they are not recommended and are not
noninformative, giving the same probability mass to implausible values as
plausible ones.
normal(location = 0, scale = NULL)
student_t(df = 1, location = 0, scale = NULL)
cauchy(location = 0, scale = NULL)
gamma(shape = 2, rate = 1)
exponential(rate = 1)
location 
Prior location. In most cases, this is the prior mean, but
for 
scale 
Prior scale. The default depends on the family (see Details). 
df 
Degrees of freedom. 
shape 
Prior shape for the gamma distribution. Defaults to 
rate 
Prior rate for the exponential distribution. Defaults to

The details depend on the family of the prior being used:
Family members:
normal(location, scale)
student_t(df, location, scale)
cauchy(location, scale)
As the degrees of freedom approaches infinity, the Student t distribution
approaches the normal distribution and if the degrees of freedom are one,
then the Student t distribution is the Cauchy distribution.
If scale
is not specified it will default to 2.5
.
A named list to be used internally by the Bernadette model fitting functions.
The vignette for the Bernadette package discusses the use of some of the supported prior distributions.
# Agespecific mortality/incidence count time series:
# Agespecific mortality/incidence count time series:
data(age_specific_mortality_counts)
data(age_specific_infection_counts)
# Import the age distribution for Greece in 2020:
age_distr < age_distribution(country = "Greece", year = 2020)
# Lookup table:
lookup_table < data.frame(Initial = age_distr$AgeGrp,
Mapping = c(rep("039", 8),
rep("4064", 5),
rep("65+" , 3)))
# Aggregate the age distribution table:
aggr_age < aggregate_age_distribution(age_distr, lookup_table)
# Import the projected contact matrix for Greece:
conmat < contact_matrix(country = "GRC")
# Aggregate the contact matrix:
aggr_cm < aggregate_contact_matrix(conmat, lookup_table, aggr_age)
# Aggregate the IFR:
ifr_mapping < c(rep("039", 8), rep("4064", 5), rep("65+", 3))
aggr_age_ifr < aggregate_ifr_react(age_distr, ifr_mapping, age_specific_infection_counts)
# Infectiontodeath distribution:
ditd < itd_distribution(ts_length = nrow(age_specific_mortality_counts),
gamma_mean = 24.19231,
gamma_cv = 0.3987261)
# Can assign priors to names:
N05 < normal(0, 5)
Gamma22 < gamma(2,2)
igbm_fit < stan_igbm(y_data = age_specific_mortality_counts,
contact_matrix = aggr_cm,
age_distribution_population = aggr_age,
age_specific_ifr = aggr_age_ifr[[3]],
itd_distr = ditd,
likelihood_variance_type = "quadratic",
prior_volatility = N05,
prior_nb_dispersion = Gamma22,
algorithm_inference = "optimizing")