Fit a brancing process strain model
Usage
fv_sample(
data,
model = forecast.vocs::fv_model(strains = 2),
diagnostics = TRUE,
...
)
Arguments
- data
A list of data as produced by
fv_as_data_list()
.- model
A
cmdstanr
model object as loaded byfv_model()
.- diagnostics
Logical, defaults to
TRUE
. Should fitting diagnostics be returned as adata.frame
.- ...
Additional parameters passed to the
sample
method ofcmdstanr
.
Value
A data.frame
containing the cmdstanr
fit, the input data, the
fitting arguments, and optionally summary diagnostics.
See also
Functions used for modelling
fv_as_data_list()
,
fv_inits()
,
fv_model()
Examples
if (FALSE) { # interactive()
options(mc.cores = 4)
# format example data
obs <- filter_by_availability(
germany_covid19_delta_obs,
date = as.Date("2021-06-12"),
)
dt <- fv_as_data_list(obs)
# single strain model
inits <- fv_inits(dt, strains = 1)
mod <- fv_model(strains = 1)
fit <- fv_sample(
dt,
model = mod, init = inits,
adapt_delta = 0.99, max_treedepth = 15
)
fit
# two strain model
inits <- fv_inits(dt, strains = 2)
mod <- fv_model(strains = 2)
two_strain_fit <- fv_sample(dt,
model = mod, init = inits,
adapt_delta = 0.99, max_treedepth = 15
)
two_strain_fit
}