prosail

An R package for the simulation of canopy reflectance using the model PROSAIL (PROSPECT+SAIL).

1 Requirements

Install devtools

Install the package devtools following the instructions depending on your operating system.

Install prospect

Install the package prospect with the following command line in R session:

devtools::install_github('jbferet/prospect')

Install liquidSVM

prosail uses Support Vector Regression (SVR) for hybrid inversion.

The default SVM implementation is currently based on the package liquidSVM. A SVM implementation based on the R package caret is also available.

liquidSVM provides very efficient and fully-integrated hyper-parameter selection, multithreading and GPU support. However, this package is not maintained anymore and may cause difficulties during the installation.

To install liquidSVM, please follow installation instructions provided in the documentation webpage.

!!! WINDOWS USERS !!!

Once liquidSVM is installed, you may need to add the 32bit DLL into the R library. This i386 directory should be downloaded here and copied into the local directory on your computer, where the binary codes of liquidSVM are installed:

Path_For_My_R_distribution/library/liquidSVM/libs/.

If liquidSVM installation fails

liquidSVM is a suggested package, so the installation of prosail should succeed even without liquidSVM. Two main functions using liquidSVM as default may be impacted: train_prosail_inversion and PROSAIL_Hybrid_Train.

If the installation of liquidSVM does not succeed, please define method = 'svmRadial' or method = 'svmLinear' as optional input variable. This will use the caret implementation, but it will require longer training stage.

2 Install prosail

The package prosail can then be installed with the following command line in R session:

devtools::install_github('jbferet/prosail')

3 Tutorial

A tutorial vignette is available here.

4 Acknowledgments / Fundings

This research was supported by the Agence Nationale de la Recherche (ANR, France) through the young researchers project BioCop (ANR-17-CE32-0001)

We thank Ingo Steinwart and Philipp Thomann (nstitute for Stochastics and Applications, University of Stuttgart, Germany) for the development of the package liquidSVM.

5 Citation

If you use prosail, please consider citing the following references when appropriate :

PROSPECT

Féret, J.-B. & de Boissieu, F. (2024). prospect: an R package to link leaf optical properties with their chemical and structural properties with the leaf model PROSPECT. Journal of Open Source Software, 9(94), 6027, https://doi.org/10.21105/joss.06027

Féret J-B, Gitelson AA, Noble SD & Jacquemoud S, 2017. PROSPECT-D: Towards modeling leaf optical properties through a complete lifecycle. Remote Sensing of Environment, 193, 204–215. https://doi.org/10.1016/j.rse.2017.03.004

Féret J-B, Berger K, de Boissieu F & Malenovský Z, 2021. PROSPECT-PRO for estimating content of nitrogen-containing leaf proteins and other carbon-based constituents. Remote Sensing of Environment, 252, 112173. https://doi.org/10.1016/j.rse.2020.112173

PROSAIL

Jacquemoud S, Verhoef W, Baret F, Bacour C, Zarco-Tejada PJ, Asner GP, François C & Ustin SL, 2009. PROSPECT+ SAIL models: A review of use for vegetation characterization. Remote Sensing of Environment, 113:S56–S66. https://doi.org/doi:10.1016/j.rse.2008.01.026

Berger K, Atzberger C, Danner M, D’Urso G, Mauser W, Vuolo F & Hank T 2018. Evaluation of the PROSAIL Model Capabilities for Future Hyperspectral Model Environments: A Review Study. Remote Sensing, 10:85. https://doi.org/10.3390/rs10010085

4SAIL & 4SAIL2

Verhoef W & Bach H, 2007. Coupled soil–leaf-canopy and atmosphere radiative transfer modeling to simulate hyperspectral multi-angular surface reflectance and TOA radiance data. Remote Sensing of Environment, 109:166-182. https://doi.org/10.1016/j.rse.2006.12.013

Verhoef W, Jia L, Xiao Q & Su Z, 2007. Unified optical-thermal four-stream radiative transfer theory for homogeneous vegetation canopies. IEEE Transactions in Geosciences and Remote Sensing, 45:1808–1822. https://doi.org/10.1109/TGRS.2007.895844

liquidSVM

Steinwart I & Thomann P (2017). liquidSVM: A Fast and Versatile SVM package. ArXiv e-prints 1702.06899, http://www.isa.uni-stuttgart.de/software

SOILSPECT

Jacquemoud S, Baret F, Hanocq J-F, 1992. Modeling spectral and bidirectional soil reflectance. Remote Sensing of Environment, 41, 123–132. https://doi.org/10.1016/0034-4257(92)90072-R