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worm_plot

Worm plot of model residuals

Description

Worm plot of model residuals

Usage

worm_plot(model, ...)

## S3 method for class 'gam'
worm_plot(
  model,
  method = c("uniform", "simulate", "normal", "direct"),
  type = c("deviance", "response", "pearson"),
  n_uniform = 10,
  n_simulate = 50,
  level = 0.9,
  ylab = NULL,
  xlab = NULL,
  title = NULL,
  subtitle = NULL,
  caption = NULL,
  ci_col = "black",
  ci_alpha = 0.2,
  point_col = "black",
  point_alpha = 1,
  line_col = "red",
  ...
)

## S3 method for class 'glm'
worm_plot(model, ...)

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

Arguments

model

a fitted model. Currently only class "gam".
...

arguments passed ot other methods.
method

character; method used to generate theoretical quantiles. Note that method = "direct" is deprecated in favour of method = "uniform".
type

character; type of residuals to use. Only "deviance", "response", and "pearson" residuals are allowed.
n_uniform

numeric; number of times to randomize uniform quantiles in the direct computation method (method = "uniform").
n_simulate

numeric; number of data sets to simulate from the estimated model when using the simulation method (method = "simulate").
level

numeric; the coverage level for reference intervals. Must be strictly 0 < level < 1. Only used with method = "simulate".
ylab

character or expression; the label for the y axis. If not supplied, a suitable label will be generated.
xlab

character or expression; the label for the y axis. If not supplied, a suitable label will be generated.
title

character or expression; the title for the plot. See ggplot2::labs().
subtitle

character or expression; the subtitle for the plot. See ggplot2::labs().
caption

character or expression; the plot caption. See ggplot2::labs().
ci_col

fill colour and alpha transparency for the reference interval when method = "simulate".
ci_alpha

fill colour and alpha transparency for the reference interval when method = "simulate".
point_col

colour and alpha transparency for points on the QQ plot.
point_alpha

colour and alpha transparency for points on the QQ plot.
line_col

colour used to draw the reference line.

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".

Examples

load_mgcv()
## simulate binomial data...
dat <- data_sim("eg1", n = 200, dist = "binary", scale = .33, seed = 0)
p <- binomial()$linkinv(dat$f)               # binomial p
n <- sample(c(1, 3), 200, replace = TRUE) # binomial n
dat <- transform(dat, y = rbinom(n, n, p), n = n)
m <- gam( y / n ~ s(x0) + s(x1) + s(x2) + s(x3),
         family = binomial, data = dat, weights = n,
         method = "REML")

## Worm plot; default using direct randomization of uniform quantiles
## Note no reference bands are drawn with this method.
worm_plot(m)

## Alternatively use simulate new data from the model, which
## allows construction of reference intervals for the Q-Q plot
worm_plot(m, method = "simulate", point_col = "steelblue",
          point_alpha = 0.4)

## ... or use the usual normality assumption
worm_plot(m, method = "normal")
gratia

Graceful 'ggplot'-Based Graphics and Other Functions for GAMs Fitted Using 'mgcv'

v0.6.0
MIT + file LICENSE
Authors
Gavin L. Simpson [aut, cre] (<https://orcid.org/0000-0002-9084-8413>), Henrik Singmann [ctb] (<https://orcid.org/0000-0002-4842-3657>)
Initial release
2021-04-17

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