Plot smooths of a GAMLSS model estimated by GJRM::gamlss

Provides a draw() method for GAMLSS (distributional GAMs) fitted by GJRM::gamlss().

Usage

# S3 method for class 'gamlss'
draw(
  object,
  scales = c("free", "fixed"),
  ncol = NULL,
  nrow = NULL,
  guides = "keep",
  widths = NULL,
  heights = NULL,
  ...,
  n = 100,
  envir = NULL,
  select = NULL,
  parametric = NULL,
  terms = NULL,
  partial_match = FALSE,
  wrap = TRUE
)

Arguments

object

a model, fitted by GJRM::gamlss()

scales

character; should all univariate smooths be plotted with the same y-axis scale? If scales = "free", the default, each univariate smooth has its own y-axis scale. If scales = "fixed", a common y axis scale is used for all univariate smooths.

Currently does not affect the y-axis scale of plots of the parametric terms.

ncol, nrow

numeric; the numbers of rows and columns over which to spread the plots

guides

character; one of "keep" (the default), "collect", or "auto". Passed to patchwork::plot_layout()

widths, heights

The relative widths and heights of each column and row in the grid. Will get repeated to match the dimensions of the grid. If there is more than 1 plot and widths = NULL, the value of widths will be set internally to widths = 1 to accommodate plots of smooths that use a fixed aspect ratio.

...

arguments passed to draw.gam()

n

numeric; the number of points over the range of the covariate at which to evaluate a univariate smooth.

envir

an optional environment supplying functions and constants used in model expressions. The available model formula environment is used when NULL. Covariate observations should be supplied in data.

select

Smooth selection across all equations, using the labels from smooths(), or numeric or logical indices in equation and smooth order. Repeated labels receive suffixes such as s.1(x); existing distinct labels are retained. partial_match uses these model-wide labels.

parametric

logical or NULL; plot parametric terms also? The default, NULL, includes parametric terms when select = NULL, but excludes them when smooths are selected explicitly. Use TRUE to include parametric terms regardless of select, or FALSE to draw only smooths (the previous default). The terms argument selects which parametric effects are plotted; select selects only smooths.

terms

character; which model parametric terms should be drawn? The Default of NULL will plot all parametric terms that can be drawn. Interactions show their individual contributions to the linear predictor; main effects and intercepts are not added. Multivariate parametric terms use the grid and surface controls below, as described in parametric_effects().

partial_match

logical; in the case of character select, should select match partially against smooths? If partial_match = TRUE, select must only be a single string, a character vector of length 1.

wrap

Logical; return an assembled patchwork when TRUE (the default), or a flat named list of plots when FALSE.

Note

For models with multiple linear predictors, smooth plot subtitles identify the distributional parameter using the parent model's margin and equation order, rather than the working family of the embedded GAMs. Single-predictor models omit these automatic labels. Existing smooth labels, selection, by-variable information and custom subtitles are retained. Pass surface = "3d", ci_3d = TRUE through ... to add interval surfaces to smooths and numeric parametric interactions in any equation. ci_3d_alpha and ci_3d_col control their opacity and fill colour.

Examples

if (suppressPackageStartupMessages(require("GJRM", quietly = TRUE))) {
  # follow example from ?GJRM::gamlss
  load_mgcv()
  suppressPackageStartupMessages(library("GJRM"))
  set.seed(0)
  n <- 100
  x1 <- round(runif(n))
  x2 <- runif(n)
  x3 <- runif(n)
  f1 <- function(x) cos(pi * 2 * x) + sin(pi * x)
  y1 <- -1.55 + 2 * x1 + f1(x2) + rnorm(n)
  dataSim <- data.frame(y1, x1, x2, x3)

  eq_mu <- y1 ~ x1 + s(x2)
  eq_s <- ~ s(x3, k = 6)
  fl <- list(eq_mu, eq_s)
  m <- gamlss(fl, data = dataSim)

  draw(m)
  if (requireNamespace("ggcube", quietly = TRUE)) {
    surface <- GJRM::gamlss(list(y1 ~ s(x2, x3, k = 10), ~ s(x3, k = 6)),
      data = dataSim)
    draw(surface, surface = "3d", ci_3d = TRUE, n_2d = 15)
  }
}