residual_plots: Several types of residual plots

In metan: Multi Environment Trials Analysis

Several types of residual plots

Description

Residual plots for a output model of class performs_ammi, waas, anova_ind, and anova_joint. Seven types of plots are produced: (1) Residuals vs fitted, (2) normal Q-Q plot for the residuals, (3) scale-location plot (standardized residuals vs Fitted Values), (4) standardized residuals vs Factor-levels, (5) Histogram of raw residuals and (6) standardized residuals vs observation order, and (7) 1:1 line plot

Usage

residual_plots(
  x,
  var = 1,
  conf = 0.95,
  labels = FALSE,
  plot_theme = theme_metan(),
  band.alpha = 0.2,
  point.alpha = 0.8,
  fill.hist = "gray",
  col.hist = "black",
  col.point = "black",
  col.line = "red",
  col.lab.out = "red",
  size.lab.out = 2.5,
  size.tex.lab = 10,
  size.shape = 1.5,
  bins = 30,
  which = c(1:4),
  ncol = NULL,
  nrow = NULL,
  ...
)

Arguments

x	An object of class performs_ammi, waas, anova_joint, or gafem
var	The variable to plot. Defaults to var = 1 the first variable of x.
conf	Level of confidence interval to use in the Q-Q plot (0.95 by default).
labels	Logical argument. If TRUE labels the points outside confidence interval limits.
plot_theme	The graphical theme of the plot. Default is plot_theme = theme_metan(). For more details, see ggplot2::theme().
band.alpha, point.alpha	The transparency of confidence band in the Q-Q plot and the points, respectively. Must be a number between 0 (opaque) and 1 (full transparency).
fill.hist	The color to fill the histogram. Default is 'gray'.
col.hist	The color of the border of the the histogram. Default is 'black'.
col.point	The color of the points in the graphic. Default is 'black'.
col.line	The color of the lines in the graphic. Default is 'red'.
col.lab.out	The color of the labels for the 'outlying' points.
size.lab.out	The size of the labels for the 'outlying' points.
size.tex.lab	The size of the text in axis text and labels.
size.shape	The size of the shape in the plots.
bins	The number of bins to use in the histogram. Default is 30.
which	Which graphics should be plotted. Default is which = c(1:4) that means that the first four graphics will be plotted.
ncol, nrow	The number of columns and rows of the plot pannel. Defaults to NULL
...	Additional arguments passed on to the function patchwork::wrap_plots().

Author(s)

Tiago Olivoto [e-mail]

Examples

library(metan)
model <- performs_ammi(data_ge, ENV, GEN, REP, GY)

# Default plot
plot(model)

# Normal Q-Q plot
# Label possible outliers
plot(model,
     which = 2,
     labels = TRUE)

# Residual vs fitted,
# Normal Q-Q plot
# Histogram of raw residuals
# All in one row
plot(model,
     which = c(1, 2, 5),
     nrow = 1)

metan documentation built on March 7, 2023, 5:34 p.m.