Plot Random Effects

Description

Generates plots of random effects from one or more fitted models contained within a GHRmodels object. The function supports two main display modes:

Caterpillar plot of effect sizes with uncertainty intervals (the default).
Choropleth map (when a spatial map (sf object) is provided in the map argument).

It also supports visualization of replicated or grouped effects via the rep_id argument.

plot_re(
  models,
  mod_id,
  re_id,
  rep_id = NULL,
  map = NULL,
  map_area = NULL,
  mod_label = NULL,
  re_label = NULL,
  rep_label = NULL,
  ref_color = NULL,
  palette = NULL,
  var_arrange = "ID",
  title = "",
  xlab = "Re ID",
  ylab = "Effect Size",
  legend = "Effect Size",
  centering = 0,
  exp = FALSE
)

Arguments

models: A GHRmodels object containing fitted models and random effects.
mod_id: Character vector of model IDs to plot (must match entries in models$mod_gof$model_id).
re_id: Character; name of the variable defining the random effect (from models$re).
rep_id: Optional character string; name of a grouping variable if random effects are replicated. Default is NULL.
map: Optional sf object providing spatial geometry. If NULL, returns a caterpillar plot.
map_area: Character; column name in map indicating spatial units (must match re_id order).
mod_label: Optional labels for models. Can be a named vector (e.g., c("mod1" = "Baseline", "mod2" = "Adjusted")) or an unnamed vector with the same order as mod_id.
re_label: Optional; variable in the data to label the random effect units (e.g., year names instead of numeric IDs).
rep_label: Optional; label for replicated grouping variable (e.g., for years or time periods).
ref_color: Color used for the reference model. If specified, this will apply to the first model in mod_id.
palette: Character; name of the color palette to use. Defaults to "IDE1" for maps and "IDE2" otherwise.
var_arrange: Character; how to arrange REs on the x-axis. Options: "median" or "ID". Default is "ID".
title: Title for the plot.
xlab: Label for the x-axis. Default is "Re ID".
ylab: Label for the y-axis. Default is "Effect Size".
legend: Label for the legend in map plots. Default is "Effect Size".
centering: Value at which to center the color scale for map plots. Default is 0.
exp: Logical; if TRUE, exponentiates the effects (useful for log-scale models). Default is FALSE.

Details

Plot Random Effects from GHRmodels

If map is used, map_area must match a column in map and correspond in order to the RE unit.
For BYM/BYM2 models, only the total random effect is plotted (structured/unstructured parts are merged).
When no map is used, the plot compares models via colored points and intervals for each RE unit.
Replicated REs (e.g., for years) can be plotted across facets using rep_label.
Model comparison is visually aided using distinct colors; the first model in mod_id is the reference.

Returns

A ggplot2 plot object:

If map is NULL, returns a caterpillar plot showing median REs with 95% uncertainty intervals.
If map is provided, returns a faceted choropleth map showing RE medians by area and (optionally) replicate.

Examples

## Not run:


# Load example GHRmodels object from the package: 
model_list_file <- system.file("examples", "model_list.rds", package = "GHRmodel")
model_list <- readRDS(model_list_file)

#  Plot the estimated yearly random effects for three different models.
plot_re(
model = model_list,                          # A GHRmodels object 
mod_id = c("mod1", "mod3", "mod5"),          # IDs of the models 

mod_label = c("Baseline",                    # Custom labels for the models
              "tmin.l1_nl",           
              "pdsi.l1_nl + tmin.l1_nl"),     

re_id = "year_id",                           # Name of the random effect variable 
re_label = "year",                           # Label to map year_id to calendar years

ref_color = "grey",                          # Color for the reference model’s effects
palette = "IDE2",                            # Color for other model effects

title = "Yearly Random Effect",              # Title for the plot
xlab = "Year"                                # Label for the x-axis 
)
## End(Not run)