plot_pairs: Pairs plot of parameters of interest and fitting diagnostics

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

Pairs plot of parameters of interest and fitting diagnostics

Description

Pairs plot of parameters of interest and fitting diagnostics

Usage

plot_pairs(
  fit,
  pars = c("r_init", "r_scale", "beta", "voc_beta", "voc_scale[1]", "init_cases[1]",
    "init_cases[2]", "eta[1]", "voc_eta[1]", "sqrt_phi[1]", "sqrt_phi[2]", "sqrt_phi"),
  diagnostics = TRUE,
  ...
)

Arguments

fit	List of output as returned by fv_sample().
pars	Character vector of parameters to try and include in the plot. Will only be included if present in the fitted model.
diagnostics	Logical, defaults to TRUE. Should fitting diagnostics be returned as a data.frame.
...	Additional parameters passed to bayesplot::mcmc_pairs().

Value

A ggplot2 based pairs plot of parameters of interest

See Also

Plotting functions add_forecast_dates(), plot.fv_forecast(), plot.fv_posterior(), plot_cases(), plot_default(), plot_growth(), plot_posterior(), plot_rt(), plot_theme(), plot_voc_advantage(), plot_voc_frac(), save_plots()

Functions to explore and validate models bp_launch_shinystan(), fv_score_forecast()

Examples

obs <- filter_by_availability(
  germany_covid19_delta_obs,
  date = as.Date("2021-06-12"),
)
dt <- fv_as_data_list(obs)
inits <- fv_inits(dt)
fit <- fv_sample(dt, init = inits, adapt_voc = 0.99, max_treedepth = 15)
plot_pairs(fit)

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