# High Throughput Phenotyping (HTP) Data Analysis

## Documentation for package ‘statgenHTP’ version 1.0.6.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

as.data.frame.TP | Coerce TP object to data.frame
countValid | Count valid observations per time point for a given trait
countValidPlot | Count valid observations per plotId for a given trait
createTimePoints | Create an object of class TP
detectSerieOut | Detect outliers for series of observations
detectSingleOut | Detect outliers for single observations
detectSingleOutMaize | detectSingleOutMaize
estimateSplineParameters | Extract estimates from fitted splines.
fitModels | Fit spatial models per time point
fitSpline | Fit Splines
fitSplineHDM | Fit P-Spline Hierarchical Curve Data Models
getCorrected | Extract corrected phenotypic values
getEffDims | Extract effective dimensions
getGenoPred | Extract predicted genotypic values
getHerit | Extract heritabilities
getTimePoints | Extract time points
getVar | Extract variances
noCorrectedRoot | Root data corrected for outliers for single observations.
PhenoarchDat1 | Greenhouse data for a maize experiment in the PhenoArch platform.
PhenovatorDat1 | Growth chamber data for an Arabidopsis experiment in the Phenovator platform.
plot.fitMod | Plot function for class fitMod
plot.HTPSpline | Plot the results of a fitted spline.
plot.psHDM | Plot function for class psHDM
plot.serieOut | Plot outliers for series of observations
plot.singleOut | Plot outliers for single observations
plot.splineEst | Plot the results of estimated spline parameters.
plot.TP | Plot function for class TP
predict.psHDM | Predict the P-Splines Hierarchical Curve Data Model
removeSerieOut | Replace outliers for series of observations by NA
removeSingleOut | Replace outliers for single observations by NA
removeTimePoints | Remove time points from an object of class TP
RootDat1 | Greenhouse data for an experiment in the RootPhAir platform.
spatCorrectedArch | Maize data corrected for spatial trends.
spatCorrectedVator | Arabidopsis data corrected for spatial trends.
spatPredArch | Maize data, genotypic predictions.
summary.fitMod | Summary function for fitMod objects
summary.TP | Summary function for TP objects