Function reference • statgenHTP

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(<splineEst>): Plot the results of estimated spline parameters.

Fit HDM splines

fitSplineHDM(): Fit P-Spline Hierarchical Curve Data Models

predict(<psHDM>): Predict the P-Splines Hierarchical Curve Data Model

plot(<psHDM>): Plot function for class psHDM

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