# plot.gamem: Several types of residual plots In metan: Multi Environment Trials Analysis

## Description

Residual plots for a output model of class gamem. Six 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. For a waasb object, normal Q-Q plot for random effects may also be obtained declaring type = 're'

## Usage

  1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 ## S3 method for class 'gamem' plot( x, var = 1, type = "res", position = "fill", rotate = FALSE, conf = 0.95, out = "print", n.dodge = 1, check.overlap = FALSE, labels = FALSE, plot_theme = theme_metan(), alpha = 0.2, fill.hist = "gray", col.hist = "black", col.point = "black", col.line = "red", col.lab.out = "red", size.line = 0.7, size.text = 10, width.bar = 0.75, 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 gamem. var The variable to plot. Defaults to var = 1 the first variable of x. type One of the "res" to plot the model residuals (default), type = 're' to plot normal Q-Q plots for the random effects, or "vcomp" to create a bar plot with the variance components. position The position adjustment when type = "vcomp". Defaults to "fill", which shows relative proportions at each trait by stacking the bars and then standardizing each bar to have the same height. Use position = "stack" to plot the phenotypic variance for each trait. rotate Logical argument. If rotate = TRUE the plot is rotated, i.e., traits in y axis and value in the x axis. conf Level of confidence interval to use in the Q-Q plot (0.95 by default). out How the output is returned. Must be one of the 'print' (default) or 'return'. n.dodge The number of rows that should be used to render the x labels. This is useful for displaying labels that would otherwise overlap. check.overlap Silently remove overlapping labels, (recursively) prioritizing the first, last, and middle labels. 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(). alpha The transparency of confidence band in the Q-Q plot. 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.line The size of the line in graphic. Defaults to 0.7. size.text The size for the text in the plot. Defaults to 10. width.bar The width of the bars if type = "contribution". 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 tiagoolivoto@gmail.com

## Examples

 1 2 3 4 5 6 library(metan) model <- gamem(data_g, gen = GEN, rep = REP, resp = PH) plot(model) 

metan documentation built on Nov. 10, 2021, 9:11 a.m.