DOI: 10.23729/5b4dc41c-eb63-4e57-9e92-191a96c54341
title: Physically-based modeling of spectral transmittance through forest canopies: data and code

description: This dataset contains the data and code that enable reproducing the results reported in article **Hovi, A., Janoutová, R., Malenovský, Z., Schraik, D., Gastellu-Etchegorry, J-P., Lauret, N., Novotný, J., Rautiainen, M., 2024. Physically-based modeling of spectral transmittance through forest canopies. Methods in Ecology and Evolution, 00, 1–14. https://doi.org/10.1111/2041-210X.14402**.

The data and code are organized in six folders as follows. 
See the README.txt in each folder for more detailed description.
- **0_spectral_transmittance_data/**
 - In situ measurements of forest canopy spectral transmittance.
- **1_model_input_data/**
 - Input data for the PARAS and DART models.
- **2_PAI_calculation/**
 - Calculation of plant area index (plant area volume density) by inverting a ray tracing model against hemispherical photographs. Used as input in the DART model. 
- **3_DART/**
 - Input data processed in formats required by the DART model, and the results of forest canopy spectral transmittance simulations with the DART model. 
 - The DART model is available as an executable file after a license agreement acceptance at https://dart.omp.eu/.
- **4_PARAS/**
 - Code for running forest canopy spectral transmittance simulations with the PARAS model, and results from those simulations.
- **5_figures_and_tables/**
 - Code for producing the figures and tables of the article.

UTF-8 encoding was used in all .txt and .csv files.

**Citation:** 

If using the code provided in this dataset, please cite this dataset and the accompanying scientific article (https://doi.org/10.1111/2041-210X.14402).

The input data (i.e., the .csv files in folders **0_spectral_transmittance_data/** and **1_model_input_data/**) were obtained from the following published open data sources.
If you use the data given in the files listed below, please credit the original data sources.
Some of the listed datasets have specific instructions for how to cite the data.
Refer to the original datasets for accurate citation information.

- Canopy transmittance and forest floor spectra, forest inventory data, hemispherical photograph, and terrestrial laser scanning data in 21 forest plots in four study areas in Finland, Estonia, and the Czech Republic, as well as accompanying foliage spectral data from the same study areas (**canopytransmittance_measurements.csv**, **canopygaps_for_PARAS.csv**, **forest_structure.csv**, **forestfloor_R.csv**, **leaf_R.csv**, **leaf_R-C1.csv**, **leaf_R-REDUCED.csv**, **leaf_R-SUNEXP.csv**, **leaf_T.csv**, **leaf_T-C1.csv**, **leaf_T-REDUCED.csv**, **leaf_T-SUNEXP.csv**, **shoot_R.csv**, **shoot_R-C1.csv**, **shoot_R-REDUCED.csv**, **shoot_R-SUNEXP.csv**, **shoot_T.csv**, **shoot_T-C1.csv**, **shoot_T-REDUCED.csv**, **shoot_T-SUNEXP.csv**, **tree_crown_dimensions_from_TLS-FINAL.csv**) were obtained from:
 - Hovi, A., Schraik, D., Hanuš, J., Lukeš, P., Lhotáková, Z., Homolová, L., & Rautiainen, M. (2024). A spectral-structural characterization of European temperate, hemiboreal and boreal forests: Laboratory and field data. Aalto University. https://doi.org/10.23729/9a8d90cd-73e2-438d-9230-94e10e61adc9
 
- Tree stem reflectance spectra (**trunk_R.csv**, **trunk_R-REDUCED.csv**) were obtained from:
 - Juola, J., Hovi, A., & Rautiainen, M. (2022). A dataset of stem bark reflectance spectra for boreal and temperate tree species. Mendeley Data, V2. https://doi.org/10.17632/pwfxgzz5fj.2
 - Lang, M., Kuusk, A., Nilson, T., Lükk, T., Pehk, M., & Alm, G. (2002). Reflectance spectra of ground vegetation in sub-boreal forests. Tartu Observatory, Estonia. http://www.aai.ee/bgf/ger2600/ (Accessed 8 October 2023).
 - Spencer, S., & Rock, B.N. (1999). BOREAS TE-08 Aspen bark spectral reflectance data. Data set. Oak Ridge National Laboratory Distributed Active Archive Center, Oak Ridge, Tennessee, U.S.A. https://doi.org/10.3334/ORNLDAAC/336 (Accessed 8 October 2023).
 
- Beta distribution parameters specifying the leaf and shoot angle distributions (**beta_distribution_parameters.csv**) were obtained from:
 - Janoutová, R., Homolová, L., Malenovský, Z., Hanuš, J., Lauret, N., & Gastellu-Etchegorry, J.P. (2019). Influence of 3D spruce tree representation on accuracy of airborne and satellite forest reflectance simulated in DART. Forests, 10, 292. https://doi.org/10.3390/f10030292
 - Pisek, J., Diaz-Pines, E., Matteucci, G., Noe, S., & Rebmann, C. (2022). On the leaf inclination angle distribution as a plant trait for the most abundant broadleaf tree species in Europe. Agricultural and Forest Meteorology, 323, 109030. https://doi.org/10.1016/j.agrformet.2022.109030
 - Pisek, J., Sonnentag, O., Richardson, A.D., & Mõttus, M. (2013). Is the spherical leaf angle distribution a valid assumption for temperate and boreal broadleaf tree species? Agricultural and Forest Meteorology, 169, 186-194. https://doi.org/10.1016/j.agrformet.2012.10.011
 - Raabe, K., Pisek, J., Sonnentag, O., & Annuk, K. (2015). Variations of leaf inclination angle distribution with height over the growing season and light exposure for eight broadleaf tree species. Agricultural and Forest Meteorology, 214-215, 2–11. http://dx.doi.org/10.1016/j.agrformet.2015.07.008
 - Stenberg, P., Smolander, H., & Kellomäki, S. (1993). Description of crown structure for light interception models: angular and spatial distribution of shoots in young Scots pine. In S. Linder and S. Kellomäki (Eds.), Management of structure and productivity of boreal and subalpine forests (pp. 43–50). Studia Forestalia Suecica 191.

- Top-of-canopy spectral irradiance and diffuse to total irradiance ratio (**total_irradiance.csv**, **diffuse_to_total_irradiance.csv**) were obtained by simulating with the libRadtran atmospheric model, with atmospheric aerosol optical depth and water vapor content derived from the data in:
 - CAMS (2023). CAMS global reanalysis (EAC4). Web page. https://ads.atmosphere.copernicus.eu/cdsapp#!/dataset/cams-global-reanalysis-eac4 (Accessed 7 October 2023).

**A note on plot naming:**

Note that the identification codes (IDs) that we used for the forest plots differ from the original dataset (https://doi.org/10.23729/9a8d90cd-73e2-438d-9230-94e10e61adc9).
Furthermore, in the published article the plots are identified just by numbers from 1 to 21 instead of full identification codes.
A conversion table is provided below.

| Plot nr in the article | Plot ID used in our computation code and in the input files (i.e., this dataset) | Plot ID used in the original dataset |
|----|--------------|--------------|
| 1 | HY_BIRCH2 | HY_BIRCH2 |
| 2 | HY_BIRCH3 | HY_BIRCH3 |
| 3 | HY_BIRCH4 | HY_BIRCH4 |
| 4 | JS_11 | JS_ALDER1 |
| 5 | JS_31 | JS_BIRCH1 |
| 6 | JS_40 | JS_BIRCH2 |
| 7 | LZ_HORNBEAM1 | LZ_HORNBEAM1 |
| 8 | LZ_MIXED3 | LZ_ASH1 |
| 9 | LZ_OAK1 | LZ_OAK1 |
| 10 | LZ_OAK4 | LZ_OAK4 |
| 11 | HY_PINE4 | HY_PINE4 |
| 12 | HY_PINE5 | HY_PINE5 |
| 13 | HY_SPRUCE3 | HY_SPRUCE3 |
| 14 | HY_SPRUCE5 | HY_SPRUCE5 |
| 15 | HY_SPRUCE6 | HY_SPRUCE6 |
| 16 | JS_21 | JS_SPRUCE1 |
| 17 | JS_37 | JS_PINE2 |
| 18 | BK_SPRUCE2 | BK_SPRUCE2 |
| 19 | BK_SPRUCE4 | BK_SPRUCE4 |
| 20 | BK_SPRUCE5 | BK_SPRUCE5 |
| 21 | BK_SPRUCE6 | BK_SPRUCE6 |

Note also that in some of the input data files there are data for one extra plot (plot ID JS_44, which corresponds to JS_BIRCH3 in the original dataset).
This plot was not used in the article, because the data from it included only one terrestrial laser scan instead of 16 scans in the other plots.