Plot crosspred Objects: Overall, Slices, or Heatmap

Description

Generate plots from a "crosspred" object. Three plot types are available:

  • type = "overall": Shows the overall exposure–response relationship, aggregated across all lags.
  • type = "slices": Produces line plots with credible interval ribbons, either across lags (for a fixed var) or across values of var (for a fixed lag).
  • type = "heatmap": Displays a two-dimensional heatmap of effects across both var and lag. Not applicable for one-basis models.
plot_coef_crosspred(
  crosspred,
  type = c("heatmap", "slices", "overall"),
  var = NULL,
  lag = NULL,
  exp = FALSE,
  palette = "-RdBu",
  n_lag_smooth = 50,
  line_color = "black",
  line_size = 0.7,
  ribbon_color = NULL,
  ribbon_alpha = 0.2,
  title = "",
  ylab = NULL,
  xlab = NULL,
  ...
)

Arguments

  • crosspred: An object of class "crosspred" or "GHR_crosspred", produced by crosspred or crosspred_inla.
  • type: Character string. Options: "overall", "slices", or "heatmap".
  • var: Optional numeric vector of exposure values (used when type = "slices" to plot across lags).
  • lag: Optional numeric vector of lag values (used when type = "slices" to plot across variables).
  • exp: Logical. If TRUE, exponentiates the results (e.g., for log or logit links).
  • palette: Character string for heatmap palette when type = "heatmap". Options: GHR, RColorBrewer or colorspace palette (e.g. “Purp”).
  • n_lag_smooth: Integer, number of interpolation points along lag for heatmap smoothing (default = 50).
  • line_color: Character string. Line color when type = "slices" or type = "overall". Default is “black”.
  • line_size: Numeric. Line width (default = 0.7).
  • ribbon_color: Character string. Color for credible interval ribbons. Defaults to line_color.
  • ribbon_alpha: Numeric. Alpha transparency for ribbons (default = 0.2).
  • title: Character string. Plot title.
  • ylab: Character string. Label for y-axis.
  • xlab: Character string. Label for x-axis.
  • ...: Additional arguments passed to ggplot2 functions.

Returns

A ggplot object for the specified plot type.

See Also

crosspred

Examples

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

# Load example cross-basis matrix from the package: 2-dimensional cross-basis matrix of the 
# non-linear effect of dengue risk across tmin values and lags: 
cb_tmin_file <- system.file("examples","cb_tmin.rds", package = "GHRmodel")
cb_tmin <- readRDS(cb_tmin_file) # loads cross-basis matrix into the environment

# Generate predictions
pred_result <- crosspred_inla(
  models    = model_dlnm,
  basis    = cb_tmin,
  mod_id = "mod2",
  at       = seq(10, 30, by = 1),  # e.g., temperature sequence
  lag      = 4,
  cen      = 20,
  ci.level = 0.95
)

# Plot DLNM predictions 
plot_coef_crosspred(
crosspred = pred_result,    # Crosspred object with model predictions
type = "slices",            # Plot temperature-specific slices of exposure-response curves
exp = TRUE,                 # Exponentiate the coefficients (to relative risk scale)
var = c(22:24),             # Display results for temperature 22°C to 24°C
line_color = "red",         # Red color for the lines representing effect estimates
line_size = 0.8,            # Line thickness set to 0.8 for better visibility
ribbon_color = "red",       # Red shading for credible interval ribbons
ribbon_alpha = 0.3,         # Set ribbon transparency to 30%
title = "Effect of minimum temperatures 22°C to 23°C on dengue relative risk by lag",
xlab = "Lag",               # Label for the x-axis (exposure variable)
ylab = "Relative Risk (RR)" # Label for the y-axis (effect estimate scale)
)