Plot the RMSPD of a cross-validation procedure

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.

Value

An object of class gg, ggplot.

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.

Author

Tiago Olivoto tiagoolivoto@gmail.com

Examples

# \donttest{
validation <- cv_ammif(data_ge2,
                       resp = EH,
                       gen = GEN,
                       env = ENV,
                       rep = REP,
                       nboot = 5)
#> 1 of 5 sets using AMMIF |==                                      | 5% 00:00:00 
2 of 5 sets using AMMIF |====                                    | 10% 00:00:00 
3 of 5 sets using AMMIF |======                                  | 15% 00:00:00 
4 of 5 sets using AMMIF |========                                | 20% 00:00:00 
5 of 5 sets using AMMIF |==========                              | 25% 00:00:01 
1 of 5 sets using AMMI2 |============                            | 30% 00:00:01 
2 of 5 sets using AMMI2 |==============                          | 35% 00:00:01 
3 of 5 sets using AMMI2 |================                        | 40% 00:00:01 
4 of 5 sets using AMMI2 |==================                      | 45% 00:00:01 
5 of 5 sets using AMMI2 |====================                    | 50% 00:00:02 
1 of 5 sets using AMMI1 |======================                  | 55% 00:00:02 
2 of 5 sets using AMMI1 |========================                | 60% 00:00:02 
3 of 5 sets using AMMI1 |==========================              | 65% 00:00:02 
4 of 5 sets using AMMI1 |============================            | 70% 00:00:03 
5 of 5 sets using AMMI1 |==============================          | 75% 00:00:03 
1 of 5 sets using AMMI0 |================================        | 80% 00:00:03 
2 of 5 sets using AMMI0 |==================================      | 85% 00:00:03 
3 of 5 sets using AMMI0 |====================================    | 90% 00:00:03 
4 of 5 sets using AMMI0 |======================================  | 95% 00:00:04 
5 of 5 sets using AMMI0 |========================================| 100% 00:00:04 

plot(validation)

# }