getCorrected: Extract corrected phenotypic values

In statgenHTP: High Throughput Phenotyping (HTP) Data Analysis

Extract corrected phenotypic values

Description

Extract corrected phenotypic values from an object of class fitMod. After fitting a spatial model at each time point, the raw phenotypic data is corrected by subtracting the (estimated) sources of variation (environmental, design effect) that are of no interest (nuisances). This allows keeping the data resolution at the plot/plant level.

Usage

getCorrected(fitMod, timePoints = names(fitMod), outFile = NULL)

Arguments

fitMod	An object of class fitMod.
timePoints	A character or numeric vector indicating the time point(s) for which the corrected values 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.
outFile	A character string indicating the .csv file to which the results should be written. If NULL no file is written.

Value

A data.frame with spatially corrected values per time point.

See Also

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

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 corrected values for one time point:
spatCorrSp <- getCorrected(modPhenoSp,
                           timePoints = 6)
head(spatCorrSp)

statgenHTP documentation built on April 14, 2023, 9:12 a.m.