High Throughput Phenotyping (HTP) Data Analysis

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Documentation for package ‘statgenHTP’ version 1.0.6.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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