Model diagnostic plots
Usage
appraise(model, ...)
# S3 method for 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 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 ofmethod = "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 topatchwork::plot_layout()
- level
numeric; the coverage level for QQ plot reference intervals. Must be strictly
0 < level < 1
. Only used withmethod = "simulate"
.- ci_alpha, ci_col
numeric; the level of alpha transparency for the QQ plot reference interval when
method = "simulate"
, or points drawn in plots.- 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()