fv_sample: Fit a brancing process strain model

In epiforecasts/forecast.vocs: Forecast Case and Sequence Notifications using Variant of Concern Strain Dynamics

Fit a brancing process strain model

Description

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 by fv_model().
diagnostics	Logical, defaults to TRUE. Should fitting diagnostics be returned as a data.frame.
...	Additional parameters passed to the sample method of cmdstanr.

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

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

epiforecasts/forecast.vocs documentation built on May 14, 2023, 2 p.m.