appraise: Model diagnostic plots

In gavinsimpson/gratia: Graceful 'ggplot'-Based Graphics and Other Functions for GAMs Fitted Using 'mgcv'

Model diagnostic plots

Description

Model diagnostic plots

Usage

appraise(model, ...)

## S3 method for class 'gam'
appraise(
  model,
  method = c("uniform", "simulate", "normal", "direct"),
  use_worm = FALSE,
  n_uniform = 10,
  n_simulate = 50,
  type = c("deviance", "pearson", "response"),
  n_bins = c("sturges", "scott", "fd"),
  ncol = NULL,
  nrow = NULL,
  guides = "keep",
  level = 0.9,
  ci_col = "black",
  ci_alpha = 0.2,
  point_col = "black",
  point_alpha = 1,
  line_col = "red",
  ...
)

## S3 method for class 'lm'
appraise(model, ...)

Arguments

model	a fitted model. Currently only class "gam".
...	arguments passed to patchwork::wrap_plots().
method	character; method used to generate theoretical quantiles. Note that method = "direct" is deprecated in favour of method = "uniform".
use_worm	logical; should a worm plot be drawn in place of the QQ plot?
n_uniform	numeric; number of times to randomize uniform quantiles in the direct computation method (method = "direct") for QQ plots.
n_simulate	numeric; number of data sets to simulate from the estimated model when using the simulation method (method = "simulate") for QQ plots.
type	character; type of residuals to use. Only "deviance", "response", and "pearson" residuals are allowed.
n_bins	character or numeric; either the number of bins or a string indicating how to calculate the number of bins.
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()
level	numeric; the coverage level for QQ plot reference intervals. Must be strictly ⁠0 < level < 1⁠. Only used with method = "simulate".
ci_alpha, ci_col	colour and transparency used to draw the QQ plot reference interval when method = "simulate".
point_col, point_alpha	colour and transparency used to draw points in the plots. See graphics::par() section Color Specification. This is passed to the individual plotting functions, and therefore affects the points of all plots.
line_col	colour specification for the 1:1 line in the QQ plot and the reference line in the residuals vs linear predictor plot.

Note

The wording used in mgcv::qq.gam() uses direct in reference to the simulated residuals method (method = "simulated"). To avoid confusion, method = "direct" is deprecated in favour of method = "uniform".

See Also

The plots are produced by functions qq_plot(), residuals_linpred_plot(), residuals_hist_plot(), and observed_fitted_plot().

Examples

load_mgcv()
## simulate some data...
dat <- data_sim("eg1", n = 400, dist = "normal", scale = 2, seed = 2)
mod <- gam(y ~ s(x0) + s(x1) + s(x2) + s(x3), data = dat)
## run some basic model checks
appraise(mod, point_col = "steelblue", point_alpha = 0.4)

## To change the theme for all panels use the & operator, for example to
## change the ggplot theme for all panels
library("ggplot2")
appraise(mod,
  point_col = "steelblue", point_alpha = 0.4,
  line_col = "black"
) & theme_minimal()

gavinsimpson/gratia documentation built on April 13, 2024, 10:56 p.m.