Plot Rhat Convergence Diagnostic

Creates a visual display of Rhat values for all parameters, with color-coding to highlight convergence issues. Rhat values > 1.01 indicate potential convergence problems.

Usage

plot_rhat(fit, threshold = 1.01, pars = NULL)

Arguments

fit

A ratiod_fit object.

threshold

Rhat threshold for warnings (default: 1.01).

pars

Character vector of parameter names to include. If NULL (default), includes all main parameters (excludes high-dimensional RE/spatial).

Value

A ggplot object (if ggplot2 available) or base R plot (invisible).

Details

Color coding:

• Green: Rhat < 1.01 (converged)

• Yellow: 1.01 <= Rhat < 1.05 (borderline)

• Red: Rhat >= 1.05 (not converged)

See also

plot_ess(), diagnostic_summary(), diagnostics()

Examples

# Diagnostic plots require a fitted ratio model
# See tratio() examples for fitting models

# \donttest{
# Fit a model (slow, not run on CRAN)
set.seed(123)
n <- 50
df <- data.frame(
  count = rpois(n, lambda = 8),
  effort = rgamma(n, shape = 4, rate = 1),
  depth = rnorm(n),
  site = factor(rep(1:10, each = 5))
)
fit <- tratio(count | effort ~ depth + (1|site), data = df,
             family = ratiod_poisson_gamma(),
             control = list(iter = 200, warmup = 100, chains = 1))
#> Inference: Exact (Tier 1)
#>   Backend: hmc
#>   Reason: default (full MCMC)
#> Fitting ratio model...
#>   Family: poisson_gamma
#>   Observations: 50
#>   Iterations: 200 (warmup: 100)
#> Running NUTS sampler...
#>   Parameters: 16
#>   Iterations: 200 (warmup: 100)
#>   Chains: 1 (cores: 1)
# plot_rhat(fit)
# }