GHRmodel (version 0.1.1)

plot_coef_nl: Plot Nonlinear Effects from a GHRmodels Object

Description

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

• Grid (when collapse = FALSE): one plot per covariate and model, with effects by column and models by row.

  • If multiple models are specified, the user must provide either name or pattern to select which nonlinear effects to plot.

  • If only one model is selected and both name and pattern are NULL, all nonlinear effects in the model will be plotted.

• Collapsed (when collapse = TRUE): one non-linear effect combined across models into a single panel.

  • The user must explicitly specify the exact variable name using name. It only accepts one covariate name.

  • Collapse mode can only be used when the selected effect is not replicated (that is, does not have the format f(covariate, model = ..., replicate = group)) If replication is detected, an error will be thrown.

Usage

plot_coef_nl(
  models,
  mod_id,
  mod_label = NULL,
  name = NULL,
  pattern = NULL,
  title = NULL,
  var_label = NULL,
  palette = "IDE2",
  xlim = NULL,
  ylab = NULL,
  xlab = NULL,
  histogram = FALSE,
  legend = NULL,
  hist_fill = "grey",
  rug = FALSE,
  collapse = FALSE,
  exp = FALSE
)

Value

A ggplot or cowplot object, depending on the plotting mode.

Arguments

models

A GHRmodels object containing fitted model outputs.

mod_id

Integer vector specifying which model(s) to plot (as indexed in model$models).

mod_label

An optional named character vector mapping model names to custom labels, e.g. c("mod1" = "Model 1"). Any model not found in the vector names retains its original label.

name

Optional character vector of variable names (as used in inla.group(...)) to select specific nonlinear effects. Required for collapse mode.

pattern

Optional regular expression pattern to match effect names. Used to select nonlinear effects when name is not provided.

title

Optional overall title for the plot.

var_label

Optional named character vector providing custom labels for each nonlinear variable. Names must match the variable names (e.g., used in inla.group(x)), not full effect names.

palette

Name of the color palette to use (passed to GHR_palette). Default is "IDE2".

xlim

Optional named list specifying x-axis limits for each effect. Each element should be a numeric vector of length 2: list(var1 = c(min, max), var2 = c(min, max)). Variable names must match those used in inla.group().

ylab

Optional y-axis label. If NULL, defaults to "Effect size".

xlab

Optional x-axis label. If NULL, defaults to "<variable> values". If explicitly set to NULL, no x-axis label will be shown.

histogram

Logical; if TRUE (default), includes a histogram below each partial-effect plot.

legend

Legend title for the replicate color scale (if multi-replicate effects are present). Default is "Replicate".

hist_fill

Fill color for histogram bars. Default is "grey".

rug

Include a rug plot in the x-axis. Default is FALSE.

collapse

Logical; if TRUE, attempts to collapse plots across models to show one plot per variable. This requires that selected nonlinear effect is not replicated (i.e. the covariate is not in the format f(covariate, model = ..., replicate = group))

exp

Logical,if TRUE the coefficients are exponentiated, Default is if FALSE.

Examples

# \donttest{
# 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 2 models with non-linear PDSI at one month lag in collapsed mode: 
plot_coef_nl(
  models = model_list,
  mod_id = c( "mod5", "mod6") ,
  mod_label = c("mod6" = "pdsi.l1_nl",
                "mod5" = "pdsi.l1_nl + tmin.l1_nl"),
  var_label = c("pdsi.l1" = "Drought index (PDSI)"),
  name = c("pdsi.l1"),
  title = "Change in PDSI with and without mean min. temp lag 1",
  xlab = "PDSI",
  palette = "IDE2",
  collapse = TRUE    
)
# }