plot.cvalidation: Plot the RMSPD of a cross-validation procedure

In metan: Multi Environment Trials Analysis

Plot the RMSPD of a cross-validation procedure

Description

Boxplot showing the Root Means Square Prediction Difference of of a cross validation procedure.

Usage

## S3 method for class 'cvalidation'
plot(
  x,
  violin = FALSE,
  export = FALSE,
  order_box = FALSE,
  x.lab = NULL,
  y.lab = NULL,
  size.tex.lab = 12,
  file.type = "pdf",
  file.name = NULL,
  plot_theme = theme_metan(),
  width = 6,
  height = 6,
  resolution = 300,
  col.violin = "gray90",
  col.boxplot = "gray70",
  col.boxplot.win = "cyan",
  width.boxplot = 0.6,
  x.lim = NULL,
  x.breaks = waiver(),
  ...
)

Arguments

x	An object of class cvalidation fitted with the functions cv_ammi(), cv_ammif(), cv_blup(), or a bound object fitted with bind_cv().
violin	Define if a violin plot is used with boxplot. Default is 'TRUE'
export	Export (or not) the plot. Default is T.
order_box	Logical argument. If TRUE then the boxplots will be ordered according to the values of the RMSPD.
x.lab	The label of x-axis. New arguments can be inserted as x.lab = 'my x label'.
y.lab	The label of y-axis. New arguments can be inserted as y.lab = 'my y label'.
size.tex.lab	The size of the text in axis text and labels.
file.type	The type of file to be exported. Default is pdf, Graphic can also be exported in *.tiff format by declaring file.type = 'tiff'.
file.name	The name of the file for exportation, default is NULL, i.e. the files are automatically named.
plot_theme	The graphical theme of the plot. Default is plot_theme = theme_metan(). For more details,see ggplot2::theme().
width	The width 'inch' of the plot. Default is 6.
height	The height 'inch' of the plot. Default is 6.
resolution	The resolution of the plot. Parameter valid if file.type = 'tiff' is used. Default is 300 (300 dpi)
col.violin	Parameter valid if violin = T. Define the color of the violin plot. Default is 'gray90.
col.boxplot	Define the color for boxplot. Default is 'gray70'.
col.boxplot.win	Define the color for boxplot of the best model. Default is 'cyan'.
width.boxplot	The width of boxplots. Default is 0.2.
x.lim	The range of x-axis. Default is NULL (maximum and minimum values of the data set). New arguments can be inserted as x.lim = c(x.min, x.max).
x.breaks	The breaks to be plotted in the x-axis. Default is authomatic breaks. New arguments can be inserted as x.breaks = c(breaks)
...	Currently not used.

Details

Five statistics are shown in this type of plot. The lower and upper hinges correspond to the first and third quartiles (the 25th and 75th percentiles). The upper whisker extends from the hinge to the largest value no further than 1.5 * IQR from the hinge (where IQR is the inter-quartile range). The lower whisker extends from the hinge to the smallest value at most 1.5 * IQR of the hinge. Data beyond the end of the whiskers are considered outlying points.

Value

An object of class gg, ggplot.

Author(s)

Tiago Olivoto [e-mail]

Examples

validation <- cv_ammif(data_ge2,
                       resp = EH,
                       gen = GEN,
                       env = ENV,
                       rep = REP,
                       nboot = 5)
plot(validation)

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