getGenoPred function

Extract predicted genotypic values

Extract predictions of the genotypic value from an object of class fitMod.

getGenoPred(
  fitMod,
  timePoints = names(fitMod),
  predictChecks = FALSE,
  outFile = NULL
)

Arguments

• fitMod: An object of class fitMod.
• timePoints: A character or numeric vector indicating the time point(s) for which the predictions should be extracted. When using a character string to reference a time point, the value has to be an exact match to one of the existing time points. When using a number it will be matched by its number ("timeNumber") in the timePoints attribute of the TP object.
• predictChecks: Should predictions of the check genotypes be included in the ouptut. If TRUE a list of two data.frames is returned from the function, one with the predictions for the regular genotypes and one with the predictions for the checks.
• outFile: A character string indicating the .csv file to which the results should be written. If NULL no file is written.

Returns

A list of two data.frames with predicted genotypic values per time point. genoPred with the predicted values for the genotypes and checkPred with the predicted values for the checks. If predictChecks = FALSE the latter will be NULL.

Examples

## Using the first example dataset (PhenovatorDat1).

phenoTP <- createTimePoints(dat = PhenovatorDat1,
                            experimentName = "Phenovator",
                            genotype = "Genotype",
                            timePoint = "timepoints",
                            repId = "Replicate",
                            plotId = "pos",
                            rowNum = "y", colNum = "x",
                            addCheck = TRUE,
                            checkGenotypes = c("check1", "check2",
                                               "check3", "check4"))

## Fit a SpATS model on few time points.
modPhenoSp <- fitModels(TP = phenoTP,
                        trait = "EffpsII",
                        timePoints = c(1, 6, 20))

## Extract the genotypic predictions for one time point:
genoPredSp <- getGenoPred(modPhenoSp,
                          timePoints = 6)
head(genoPredSp)

See Also

Other functions for spatial modeling: fitModels(), getCorrected(), getEffDims(), getHerit(), getVar(), plot.fitMod(), summary.fitMod()