Data preparation

createTimePoints()

Create an object of class TP

plot(<TP>)

Plot function for class TP

summary(<TP>)

Summary function for TP objects

getTimePoints()

Extract time points

removeTimePoints()

Remove time points from an object of class TP

as.data.frame(<TP>)

Coerce TP object to data.frame

Detect outliers for single observations

detectSingleOut()

Detect outliers for single observations

removeSingleOut()

Replace outliers for single observations by NA

plot(<singleOut>)

Plot outliers for single observations

detectSingleOutMaize()

detectSingleOutMaize

Spatial modeling

fitModels()

Fit spatial models per time point

plot(<fitMod>)

Plot function for class fitMod

summary(<fitMod>)

Summary function for fitMod objects

getGenoPred()

Extract predicted genotypic values

getCorrected()

Extract corrected phenotypic values

getHerit()

Extract heritabilities

getVar()

Extract variances

getEffDims()

Extract effective dimensions

Fit splines

fitSpline()

Fit Splines

plot(<HTPSpline>)

Plot the results of a fitted spline.

Estimate parameters

estimateSplineParameters()

Extract estimates from fitted splines.

plot(<HTPSplineEst>)

Plot the results of estimated spline parameters.

Detect outliers for series of observations

detectSerieOut()

Detect outliers for series of observations

removeSerieOut()

Replace outliers for series of observations by NA

plot(<serieOut>)

Plot outliers for series of observations

Example data

PhenoarchDat1

Greenhouse data for a maize experiment in the PhenoArch platform.

PhenovatorDat1

Growth chamber data for an Arabidopsis experiment in the Phenovator platform.

RootDat1

Greenhouse data for an experiment in the RootPhAir platform.

spatCorrectedArch

Maize data corrected for spatial trends.

spatCorrectedVator

Arabidopsis data corrected for spatial trends.

noCorrectedRoot

Root data corrected for outliers for single observations.

spatPredArch

Maize data, genotypic predictions.

Utility functions

countValid()

Count valid observations per time point for a given trait

countValidPlot()

Count valid observations per plotId for a given trait