canObsR is a R package which aims at streamlining, standardizing and facilitating processing of repetead UAV surveys. It notably allows generating 3D and 4D mosaics & mosaics spatial alignment using state-of-the-art approaches. canObsR is also used to do phenological monitoring at the individual tree level. It gives tools to build a database with pictures of individual crown overtime, spectral indices of crowns overtime, add labels to classify pictures and analyse the phenological and the spectral data.
The installation of canObsR involves several steps that go beyond a typical R package to ensure seamless integration between R, Python and Metashape. To avoid dependency conflicts and enabling the package’s full functionality you must follow the installation guide.
Installations steps :
- Install R, Rstudio, Rtools
- Install reticulate package in R
- Install canObsR package in R
- Install miniconda or Anaconda
- Create conda environment from “canobsR/PYTHON/environment.yaml”
- Install Metashape python API
- Activate Metashape in your conda environment
canObsR workflow is represented by the Fig.1. The documentation associated to each part of the workflow is mentioned by an * in the figure and the differents links are available just below in the “Documentation” section. The functionalities shows by transparent background rectangles are still being developed.
Fig.1 : canObsR workflow
All the R package documentation is available here.
The following articles are available :
- Prepare database
- Generate and align ortomosaics
- Create compatible crown delineation file
- Generate crown labels
- Generate crown indices
- Visualize data
And the Reference section stores all the documentation about the functions.
To cite ‘canObsR’, please use citation(‘canObsR’).