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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

339

Version

1.0.8

License

GPL

Issues

0

Pull Requests

0

Stars

5

Forks

1

Maintainer

Bart-Jan van Rossum

Last Published

April 29th, 2025

Functions in statgenHTP (1.0.8)

detectSingleOut

Detect outliers for single observations
detectSingleOutMaize

detectSingleOutMaize
countValid

Count valid observations per time point for a given trait
countValidPlot

Count valid observations per plotId for a given trait
fitSplineHDM

Fit P-Spline Hierarchical Curve Data Models
getGenoPred

Extract predicted genotypic values
getEffDims

Extract effective dimensions
estimateSplineParameters

Extract estimates from fitted splines.
getVar

Extract variances
getCorrected

Extract corrected phenotypic values
fitSpline

Fit Splines
fitModels

Fit spatial models per time point
getTimePoints

Extract time points
getHerit

Extract heritabilities
plot.fitMod

Plot function for class fitMod
removeSerieOut

Replace outliers for series of observations by NA
noCorrectedRoot

Root data corrected for outliers for single observations.
predict.psHDM

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

Plot outliers for series of observations
plot.singleOut

Plot outliers for single observations
plot.HTPSpline

Plot the results of a fitted spline.
plot.TP

Plot function for class TP
plot.splineEst

Plot the results of estimated spline parameters.
plot.psHDM

Plot function for class psHDM
spatCorrectedVator

Arabidopsis data corrected for spatial trends.
summary.TP

Summary function for TP objects
removeSingleOut

Replace outliers for single observations by NA
removeTimePoints

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

Summary function for fitMod objects
spatPredArch

Maize data, genotypic predictions.
statgenHTP-package

statgenHTP: High Throughput Phenotyping (HTP) Data Analysis
spatCorrectedArch

Maize data corrected for spatial trends.
PhenoarchDat1

Greenhouse data for a maize experiment in the PhenoArch platform.
createTimePoints

Create an object of class TP
detectSerieOut

Detect outliers for series of observations
as.data.frame.TP

Coerce TP object to data.frame
RootDat1

Greenhouse data for an experiment in the RootPhAir platform.
PhenovatorDat1

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