generate_obs: Generate Simulated Observations

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

Generate Simulated Observations

Description

Generate simulated observations from the prior or posterior distributions of a forecast.vocs model. When a single strain model is used only case data is simulated but when a multiple strain model is used sequence data is also simulated.

Usage

generate_obs(
  obs,
  strains = 2,
  model = forecast.vocs::fv_model(strains = strains),
  data_list = forecast.vocs::fv_as_data_list,
  inits = forecast.vocs::fv_inits,
  fit = forecast.vocs::fv_sample,
  type = "prior",
  datasets = 10,
  ...
)

Arguments

obs	Observed data to use to parameterise the model and used for fitting when the posterior is required.
strains	Integer number of strains to use. Defaults to 2. Current maximum is 2. A numeric vector can be passed if forecasts from multiple strain models are desired.
model	A cmdstanr model object as loaded by fv_model().
data_list	A function that returns a list of data as ingested by the inits and fit function. Must use arguments as defined in fv_as_data_list(). If not supplied the package default fv_as_data_list() is used.
inits	A function that returns a function to samples initial conditions with the same arguments as fv_inits(). If not supplied the package default fv_inits() is used.
fit	A function that fits the supplied model with the same arguments and return values as fv_sample(). If not supplied the package default fv_sample() is used which performs MCMC sampling using cmdstanr.
type	A character string indicating the type of data to generate. Supported options are data based on the "prior" or data based on the "posterior" with the default being the prior.
datasets	Numeric, defaults to 10. Number of datasets to generate.
...	Additional arguments to pass fv_as_data_list().

Value

A dataframe with a sampled dataset on each row with the following variables: parameters (prior/posterior parameters used to generate the data), obs (simulated observed data), data, (the simulated data formatted using the supplied data_list function (by default fv_as_data_list()) with the same arguments as specified for simulation).

See Also

Functions to generate simulated data sample_sequences()

Examples

options(mc.cores = 4)
obs <- latest_obs(germany_covid19_delta_obs)

sim_obs <- generate_obs(obs, voc_scale = c(0.8, 0.1), r_init = c(-0.1, 0.05))

# fit a simulated dataset
sim_dt <- sim_obs$data[[1]]
inits <- fv_inits(sim_dt)
fit <- fv_sample(
  sim_dt,
  init = inits, adapt_delta = 0.95, max_treedepth = 15
)

# summarise and plot simualated fit
posterior <- fv_tidy_posterior(fit)

plot_cases(posterior, log = TRUE)

plot_voc(posterior)

plot_rt(posterior)

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