Résumé
### Update 03/02/2025: the most up to date version of the processing pipeline presented here, also working on Linux, is available on github: https://github.com/fischer-fjd/GCA/tree/main, and a worked example with open data from the Dutch AHN surveys is available on Zenodo: https://zenodo.org/records/14722001 ###
This is a collection of scripts and research data to assess the robustness of forest structure characterization from airborne laser scanning (ALS). It accompanies the article "Robust characterization of forest structure from airborne laser scanning – a systematic assessment and sample workflow for ecologists" (accepted in Methods in Ecology and Evolution on 25/08/2024).
In the article, we assess the derivation of canopy height models (CHMs) from point cloud data, how sensitive CHM algorithms are to point cloud degradation (pulse density thinning, large scan angles, loss of higher-order returns) and how uncertainties and biases propagate to commonly used forest structure metrics. In addition, we provide a standardized processing pipeline in R to convert point clouds into CHMs.
The main data source for this study are ALS point clouds from nine Australian research sites belonging to the Terrestrial Ecosystem Research Network (TERN, 5 km x 5 km extent each). The underlying data can be found here: https://portal.tern.org.au/metadata/TERN/4ff0b4c9-cfa0-4d09-9520-b5402adc583f. For one site (Robson Creek), we also used field data to assess the sensitivity of aboveground biomass estimates to ALS point cloud characteristics. Data are available here: https://portal.tern.org.au/metadata/supersite.174.
To characterize climatic/environmental differences between sites, we used climatic data from the CHELSA/BIOCLIM+ climatology 1981-2010 (Brun et al. 2022: Global climate-related predictors at kilometer resolution for the past and future. Earth System Science Data, 14(12), 5573–5603. https://doi.org/10.5194/essd-14-5573-2022; Karger et al. 2017: Climatologies at high resolution for the earth's land surface areas. Scientific Data, 4(1), 170122. https://doi.org/10.1038/sdata.2017.122).
We note that the enormous size of the full set of manipulated point clouds (original + thinned + individual flightlines: ~400 GB) and the derived raster products (~200 GB) by far exceeds limits on data storage in Zenodo. However, all analyses can be recreated from scratch from the openly available data and the R code in this repository. In addition, we include derived products for the nine study sites that allow to replicate results in the main text without any point cloud processing (CHMs and other rasters across thinned point clouds + summary statistics).
The different data layers are:
01_rscripts.zip:
contains a sample script to test the processing pipeline (test.processing.R) as well as a collection of helper functions (ALS_processing_helperfunctions_v40.R); the script can be run directly after unzipping the folder, but an installation of LAStools (https://rapidlasso.de) is necessary (path_lastools = "PATH/TO/LASTOOLS/BIN"); we note that the script was developed on Windows PCs, its application with the recent Linux distribution of LAStools has not yet been tested
contains the full set of scripts necessary to reproduce the analyses, including point cloud manipulations and derivation of CHMs from the raw data (create.CHMs.R) as well as the overall robustness analysis (analyze.CHMs.R); to replicate the processing of the raw point clouds step by step, .laz files should be downloaded from the TERN repository (cf. citation above) and placed in a "data" folder, with subfolders for each site and with the same naming conventions as in this repository (e.g., "/data/Alice Mulga")
02_reference.zip
contains reference digital surface models (DSMs), canopy height models (CHMs) and digital terrain models (DTMs) for all nine TERN sites, based on the original ALS point clouds
note that these reference layers are produced with the "CHMhighest" algorithm, which provides an easily interpretable canopy description as long as pulse densities are high (>= 20 shots per squaremetre)
03_climate.zip
contains site coordinates
contains the climate layers from the CHELSA climatology (cf. citation above, only used to evaluate climatic ranges of sites)
04_robson_additional.zip
contains biomass estimates for Robson Creek
contains shapefiles for large trees at Robson Creek (only used for visualization purposes)
05_downsampling_pulse_[Site name].zip
[Site name] is a stand-in for the nine TERN sites (e.g., "Alice Mulga.zip", "Credo.zip", etc.)
contains the data necessary to reproduce results in the main text of the study, i.e. DSMs, CHMs, and DTMs for all nine TERN sites, and at different pulse density levels (from 16 down to 0.5 laser shots per squaremetre)
also contains calculated summary statistics for each site
All zip files should be extracted into the same folder, except for 05_downsampling_pulse_[Site name].zip which should all be moved to a subfolder called "downsampling_pulse".