plotResiduals: Plot a series of residual plots obtained from a linear mixed...
In digiYozhik/msc_thesis: Functions to support master thesis

Description Usage Arguments Value Author(s) References See Also

Plot a series of residual plots obtained from a linear mixed model

1 2	plotResiduals(x, residuals, by, rows = "ROW", ranges = "RANGE", trimVariogram = FALSE, trait = NULL)

`x`	A data frame that contains at least the columns `residuals`, `ROW`, `RANGE` and `by`.
`residuals`	Character string specifying the column name of the residuals in `x`.
`by`	Character string specifying the column name for the splitting factor in `x`, usually this is a location factor.
`rows`	Character string specifying the column name with the `ROW`- coordinates in x. Default = "ROW".
`ranges`	Character string specifying the column name with the `RANGE`-coordinates in x. Default = "RANGE".
`trimVariogram`	Logical indicating whether to trim the variogram to shorter lag values. Default = "FALSE".
`trait`	Character string specifying the trait name to use in the title for the plots. Default to `NULL`, in which case no secondary title with trait name is printed.

Produces various diagnostic residual plots. The colors are scaled to be comparable over different by-levels (if there are). Four plots are outputted per location and are shown in the graphical device. The plots are listed below and detailed about the construction and use is given in Appendix A in the referred thesis.

plot upper-left: Variogram of the residuals for the rows and ranges. By default the lags are limited by 30.
plot upper-right: Conditional residual plots, colored by their value and sign.
plot bottom-left: Scatterplot of the the residuals against the range number conditional on the row number
plot bottom-right: Scatterplot of the the residuals against the row number conditional on the range number

Ruud Derijcker, Krishna Bondalapati

Derijcker, R. (2015). Investigating incorporation of genotype x environment interaction (G x E) for genomic selection in a practical setting. Unpublished M.Sc. thesis. University of Ghent: Belgium.

plotVariogram.

digiYozhik/msc_thesis documentation built on May 14, 2019, 5:16 p.m.