tidy.mvgam: Tidy an `mvgam` object's parameter posteriors

Description

Get parameters' posterior statistics, implementing the generic tidy from the package broom.

Usage

# S3 method for mvgam
tidy(x, probs = c(0.025, 0.5, 0.975), ...)

Value

A tibble containing:

"parameter": The parameter in question.
"type": The component of the model that the parameter belongs to (see details).
"mean": The posterior mean.
"sd": The posterior standard deviation.
percentile(s): Any percentiles of interest from these posteriors.

Arguments

x: An object of class mvgam.
probs: The desired probability levels of the parameters' posteriors. Defaults to c(0.025, 0.5, 0.975), i.e. 2.5%, 50%, and 97.5%.
...: Unused, included for generic consistency only.

Details

The parameters are categorized by the column "type". For instance, the intercept of the observation model (i.e. the "formula" arg to mvgam()) has the "type" "observation_beta". The possible "type"s are:

observation_family_extra_param: any extra parameters for your observation model, e.g. sigma for a gaussian observation model. These parameters are not directly derived from the latent trend components (contrast to mu).
observation_beta: betas from your observation model, excluding any smooths. If your formula was y ~ x1 + s(x2, bs='cr'), then your intercept and x1's beta would be categorized as this.
random_effect_group_level: Group-level random effects parameters, i.e. the mean and sd of the distribution from which the specific random intercepts/slopes are considered to be drawn from.
random_effect_beta: betas for the individual random intercepts/slopes.
trend_model_param: parameters from your trend_model.
trend_beta: analog of "observation_beta", but for any trend_formula.
trend_random_effect_group_level: analog of "random_effect_group_level", but for any trend_formula.
trend_random_effect_beta: analog of "random_effect_beta", but for any trend_formula.

Additionally, GP terms can be incorporated in several ways, leading to different "type"s (or absence!):

s(bs = "gp"): No parameters returned.
gp() in formula: "type" of "observation_param".
gp() in trend_formula: "type" of "trend_formula_param".
GP() in trend_model: "type" of "trend_model_param".

Examples

Run this code

if (FALSE) {
set.seed(0)
simdat <- sim_mvgam(
  T = 100,
  n_series = 3,
  trend_model = AR(),
  prop_trend = 0.75,
  family = gaussian()
)

simdat$data_train$x <- rnorm(nrow(simdat$data_train))
simdat$data_train$year_fac <- factor(simdat$data_train$year)

mod <- mvgam(
  y ~ -1 + s(time, by = series, bs = 'cr', k = 20) + x,
  trend_formula = ~ s(year_fac, bs = 're') - 1,
  trend_model = AR(cor = TRUE),
  family = gaussian(),
  data = simdat$data_train,
  silent = 2
)

tidy(mod, probs = c(0.2, 0.5, 0.8))
}