{exploreHTP}

{exploreHTP} is an R Shiny application designed to support the processing and analysis of high-throughput phenotyping data obtained from UAV imagery. It also integrates modeling functionality from {flexFitR} to fit nonlinear models to plant growth trajectories.

Installation

You can install the development version of {exploreHTP} from GitHub using:

# install.packages("pak")
pak::pkg_install("AparicioJohan/exploreHTP")

Run

You can launch the application by running:

library(exploreHTP)
run_app()

Input file formats

{exploreHTP} supports the following input files:

• RGB orthomosaics: GeoTIFF (.tif)
• Digital Surface Models (DSM): GeoTIFF (.tif)
• Multispectral orthomosaics: multiband GeoTIFF (.tif)
• Plot boundaries: GeoPackage (.gpkg) containing polygon features representing individual experimental plots

Plot boundary files can be created using GIS software such as QGIS.

Video tutorials

Step-by-step video tutorials are available on the UW Potato Breeding YouTube channel.

Image Analysis playlist

Watch the complete tutorial series in the Image Analysis playlist.

Available tutorials

1. Installing exploreHTP for UAV imagery analysis

2. Extracting ground cover and plant height with exploreHTP

3. Estimating emergence time and time to canopy closure

4. Extracting NDVI from multispectral UAV imagery with exploreHTP

5. Estimating senescence time using the GLI vegetation index

6. Fitting logistic growth models to UAV-derived ground cover data

Additional tutorials will be added to the playlist as they become available.

Getting help and reporting issues

Questions, bug reports, feature requests, and suggestions are welcome through the GitHub Issues page.

Before submitting a new issue:

1. Search the existing issues to check whether the problem has already been reported.
2. Confirm that you are using the most recent version of {exploreHTP}.
3. Restart R and verify that the problem can be reproduced.
4. Prepare a small reproducible example whenever possible.

Browse existing issues

Submit a new issue

About

You are reading the documentation for version: 1.0.0

This README was compiled on:

Sys.time()
#> [1] "2026-08-12 10:19:11 CDT"