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statgenHTP

statgenHTP is developed as an easy-to-use package for analyzing data coming from high throughput phenotyping (HTP) platform experiments. The package provides many options for plotting and exporting the results of the analyses. It was developed within the EPPN2020 project to meet the needs for automated analyses of HTP data.

Installation

  • Install from CRAN:
install.packages("statgenHTP")
  • Install latest development version from GitHub (requires remotes package):
remotes::install_github("Biometris/statgenHTP", ref = "develop", dependencies = TRUE)

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Version

Install

install.packages('statgenHTP')

Monthly Downloads

295

Version

1.0.9.1

License

GPL

Issues

0

Pull Requests

0

Stars

6

Forks

2

Maintainer

Bart-Jan van Rossum

Last Published

July 3rd, 2025

Functions in statgenHTP (1.0.9.1)

fitSpline

Fit Splines
getTimePoints

Extract time points
estimateSplineParameters

Extract estimates from fitted splines.
getCorrected

Extract corrected phenotypic values
getVar

Extract variances
getEffDims

Extract effective dimensions
getGenoPred

Extract predicted genotypic values
getHerit

Extract heritabilities
fitSplineHDM

Fit P-Spline Hierarchical Curve Data Models
fitModels

Fit spatial models per time point
plot.TP

Plot function for class TP
predict.psHDM

Predict the P-Splines Hierarchical Curve Data Model
plot.fitMod

Plot function for class fitMod
removeSerieOut

Replace outliers for series of observations by NA
plot.serieOut

Plot outliers for series of observations
plot.psHDM

Plot function for class psHDM
plot.splineEst

Plot the results of estimated spline parameters.
plot.singleOut

Plot outliers for single observations
noCorrectedRoot

Root data corrected for outliers for single observations.
plot.HTPSpline

Plot the results of a fitted spline.
removeSingleOut

Replace outliers for single observations by NA
removeTimePoints

Remove time points from an object of class TP
summary.TP

Summary function for TP objects
spatPredArch

Maize data, genotypic predictions.
statgenHTP-package

statgenHTP: High Throughput Phenotyping (HTP) Data Analysis
summary.fitMod

Summary function for fitMod objects
spatCorrectedVator

Arabidopsis data corrected for spatial trends.
spatCorrectedArch

Maize data corrected for spatial trends.
RootDat1

Greenhouse data for an experiment in the RootPhAir platform.
detectSingleOutMaize

detectSingleOutMaize
as.data.frame.TP

Coerce TP object to data.frame
detectSingleOut

Detect outliers for single observations
countValidPlot

Count valid observations per plotId for a given trait
detectSerieOut

Detect outliers for series of observations
createTimePoints

Create an object of class TP
countValid

Count valid observations per time point for a given trait
PhenovatorDat1

Growth chamber data for an Arabidopsis experiment in the Phenovator platform.
PhenoarchDat1

Greenhouse data for a maize experiment in the PhenoArch platform.