DOI: 10.5281/zenodo.14768398
title: Initial conditions for the ED2 model, derived from airborne laser scanning, Brazilian Amazon, 2016

description: Summary

This dataset provides regional distribution forest structure characteristics across the Brazilian Amazon that were derived from 545 airborne lidar transects (300 x 12500 m each) acquired during the Amazon Biomass Estimation Project (EBA2016) campaign in 2016, and described in Görgens et al. (2021). These datasets contain vertical distributions of stem number density, aboveground biomass and potential leaf area index for over 1,300,000 columns (50 × 50 m each) that were aggregated into 288 grid cells (1×1°) based on the geographic location. The data are reported in text format that is fully compatible with the initial conditions files for initialising the Ecosystem Demography Model (ED2; Longo et al. 2019), using the method described in Longo et al. (2020).

You need to download and uncompress all three files to use it with the ED2 model.

Relevant publication

Longo, M., M. Keller, L. M. Kueppers, K. Bowman, O. Csillik, A. Ferraz, P. R. Moorcroft, J. P. Ometto, B. S. Soares-Filho, X. Xu, M. L. F. de Assis, E. B. Görgens, E. J. L. Larson, J. F. Needham, E. M. Ordway, F. R. S. Pereira, E. Rangel Pinagé, L. Sato, L. Xu, and S. Saatchi. 2025. Degradation and Deforestation Increase the Sensitivity of the Amazon Forest to Climate Extremes, in review.

Dataset Overview

This dataset provides regional distribution forest structure characteristics across the Brazilian Amazon that were derived from 545 airborne lidar transects (300 × 12500 m each) acquired during the Amazon Biomass Estimation Project (EBA2016) campaign in 2016. These datasets contain vertical distributions of stem number density, aboveground biomass and potential leaf area index for over 1,300,000 columns (50 × 50 m each) that were aggregated into 288 grid cells (1 × 1°) based on the geographic location. The data are reported in text format that is fully compatible with the initial conditions files for initializing the Ecosystem Demography Model (ED2).

To generate this dataset, the discrete-return point cloud of each airborne lidar transect was split into multiple 50 × 50 m columns. Following the same methodology as in Longo et al. (2020), we used a waveform simulator and a light extinction model to retrieve vertical profiles of plant area density (PAD), and used the characteristics of the PAD curves to split the profiles into multiple size-dependent cohorts. Based on the cohort height and plant area index (PAI), we estimated leaf area index, stem number density and biomass of each cohort (Longo et al., 2020). We assigned each column to one grid cell (1 × 1°) based on the geographic location of each column. This resulted in 288 grid cells with at least one vertical profile across the Brazilian Amazon. The vertical profiles were also assigned to different sites within the grid cell, which are based on soil characteristics, as described in Longo et al. (2025).

Data characteristics



Spatial Coverage: Brazilian Amazon Biome (74°W–45°W; 14°S–5°N)

Spatial Resolution: 1° (grid cell) and sub-grid samples (50 m each)

Temporal coverage: 2016

Temporal Resolution: N/A


Data file information

There are 288 sets of files organized in 3 TAR/GZIP archives corresponding to the level of aggregation (sites, patches, cohorts). Each grid cell set contains 3 ASCII files, with extensions sss (site file), pss (patch file), and css (cohort file). These three files are formatted following the Ecosystem Demography Model convention for multi-site initial conditions (NL%IED_INIT_MODE=8) and described in detail here.

 

The files are named amzbr_GGGG.latLATlonLON.EEE, where



GGGG = grid cell identifier

LAT = latitude of the grid cell centre in decimal degrees

LON = longitude of the grid cell centre in decimal degrees

EEE = file extension (either sss, pss, or css)


For example, the file amzbr_0006.lat-12.5lon-60.5.css contains the cohort-level forest structure for grid cell ID 6, located at 12.5°S and 60.5°W. Note that not every ID between 1 and 350 exists, because some grid cells had no overlap with any lidar transect. The contents of each patch, site, and cohort file are described in Tables 1–3.

Data file details

Table 1. Variables in the site files (extension sss)






Variable



Unit



Description





time



years



Year





site



string



Unique site identifier, consistent with pss/css files for the same grid cell





area



fraction



Fraction of the grid cell area represented by site





depth



m



Soil depth to bedrock (Pelletier et al., 2016)





nscol



integer



Soil colour (Lawrence et al., 2007). Soil colour classes describe the albedo. Possible values go from 1 to 20, with 1 being the class with the highest albedo, and 20 being the one with the lowest albedo.





ntext



integer



Soil texture class (Poggio et al., 2021). Possible values, based on ED2 defaults (Longo et al., 2019) are

1. Sand

2. Loamy sand

3. Sandy loam

4. Silt loam

5. Loam

6. Sandy clay loam

7. Silty clay loam

8. Clay loam

9. Sandy clay

10. Silty clay

11. Clay

14. Silt

15. Heavy clay

16. Clayey sand

17. Clayey silt





sand



fraction



Sand fraction (Poggio et al., 2021)





clay



fraction



Clay fraction (Poggio et al., 2021)





slsoc



kg kg−1



Mass fraction of soil organic carbon (Poggio et al., 2021)





slph



pH



Soil acidity (Poggio et al., 2021)





slcec



mol kg−1



Cation exchange capacity (Poggio et al., 2021)





sldbd



kg m−3



Dry bulk density (Poggio et al., 2021)





elevation



m



Terrain elevation (dummy value, reserved field for future ED2-TOPMODEL implementation)





slope



degrees



Terrain slope  (dummy value, reserved field for future ED2-TOPMODEL implementation)





aspect



degrees



Terrain aspect (dummy value, reserved field for future ED2-TOPMODEL implementation)





TCI



dimensionless



Topography convergence index (dummy value, reserved field for future ED2-TOPMODEL implementation)





moist_f



m−1



Rate of exponential decay of soil conductance with depth (dummy value, reserved field for future ED2-TOPMODEL implementation)





moist_w



dimensionless



Soil wetness index (dummy value, reserved field for future ED2-TOPMODEL implementation)





 

Table 2. Variables in the patch files (extension pss).






Variable



Unit



Description





time



years



Year





site



string



Unique site identifier (consistent with sss/css files)





patch



string



Unique patch identifier (consistent with sss/css files). Patch names use the following convention: EBA_TNtttt_yyyy_uuu_Xeeeeeeee_Ynnnnnnnn where

tttt = EBA2016 transect number

yyyy = year of the lidar acquisition

uuu = UTM zone (and hemisphere)

eeeeeeee = Easting of the column centre (m)nnnnnnnn = Northing of the column centre (m)





dtype



integer



Disturbance type. Allowed classes are 

1. Pasture

2. Forest plantation

3. Tree fall

4. Burnt patch

5. Abandoned managed land

6. Logged forest (felling)

7. Skid trails (felling)

8. Cropland 





age



years



Patch age since last disturbance





area



fraction



Fractional area represented by patch. The sum of the areas of all patches within the same site add up to 1.





fgc



kgC m−2



Fast soil carbon (above ground). Estimated from land use history and literature search (Longo et al., 2020).





fsc



kgC m−2



Fast soil carbon (below ground). Estimated from land use history and literature search (Longo et al., 2020).





stgc



kgC m−2



Structural soil carbon (above ground). Estimated from land use history and literature search (Longo et al., 2020).





stgl



kgL m−2



Structural soil lignin (above ground). Estimated from land use history and literature search (Longo et al., 2020).





stsc



kgC m−2



Structural soil carbon (below ground). Estimated from land use history and literature search (Longo et al., 2020).





stsl



kgL m−2



Structural soil lignin (below ground). Estimated from land use history and literature search (Longo et al., 2020).





msc



kgC m−2



Microbial soil carbon. Estimated from land use history and literature search (Longo et al., 2020).





ssc



kgC m−2



Humified (slow) soil carbon. Estimated from land use history and literature search (Longo et al., 2020).





psc



kgC m−2



Passive (very slow) soil carbon. Estimated from land use history and literature search (Longo et al., 2020).





fsn



kgN m−2



Fast soil nitrogen (below and above ground). Estimated from land use history and literature search (Longo et al., 2020).





msn



kgN m−2



Mineralised soil nitrogen. Estimated from land use history and literature search (Longo et al., 2020).





npl



m−2



Total stem number density in this patch (consistent with the css file).





agb



kgC m−2



Aboveground biomass carbon density in this patch (consistent with the css file).





lai



m2 m−2



Leaf area index in this patch (consistent with the css file)





 

Table 3. Variables in the cohort files (extension css).






Variable



Unit



Description





time



years



Year





site



string



Unique site identifier (consistent with sss/pss files)





patch



string



Unique patch identifier (consistent with sss/pss files).

 





cohort



Integer



Cohort index in the patch





dbh



cm



Diameter at breast height





height



m



Plant height





pft



integer



Plant functional type, consistent with ED2 default classes. Possible values are:

1. Tropical C4 grass

2. Early-successional, evergreen broadleaf tropical tree

3. Mid-successional, evergreen broadleaf tropical tree

4. Late-successional, evergreen broadleaf tropical tree





nplant



m−2



Total stem number density of this cohort





bdead



kgC



Biomass stored in heartwood (structural, dead tissues)





balive



kgC



Biomass stored in living tissues (leaves, fine roots, sapwood, bark)





agb



kgC



Aboveground biomass of this cohort





lai



m2 m−2



(Maximum) Leaf area index of this cohort





Application and derivation

These files are intended to provide initial conditions for cohort-based vegetation demography models. Vegetation structure data (stem number density, aboveground biomass, leaf area index) were obtained from airborne lidar surveys following the method described in Longo et al. (2020) and extensively cross-validated. Soil edaphic characteristics are obtained from existing datasets (Lawrence et al., 2007, Pelletier et al., 2016; Poggio et al., 2021), and users are referred to these publications for uncertainty. Carbon stored in litter and soil layers (patch files) were estimated from the land use history and limited measurements in different land use types. These data are provided here because these quantities are required by ED2, but their uncertainty is likely very high and unlikely to provide reliable information at regional scale.

Quality assessment

Results using regional cross-validation (i.e., bootstrapping sampling that sets entire regions as testing) showed that the approach produces realistic variability in forest structures in the Amazon, both across precipitation gradients and at different levels of forest degradation (Longo et al., 2020).

Data Acquisition, Materials, and Methods

To turn raw airborne lidar dataset into forest structure distributions, we used the same approach described in Longo et al. (2020). We pooled airborne lidar data from the EBA campaign archive, publicly available through Ometto et al. (2023), selected only the transects designated for random sampling (545 transects). Each transect was split into multiple 50 × 50 m columns, resulting in 1,310,478 columns. Each column was assumed to be one patch. For each patch, we simulated waveforms using an approach similar to the GEDI waveform simulator (Hancock et al., 2019) and applied a light extinction model based on Ni-Meister et al. (2001) to derive a first guess of leaf area density (LAD). We used the lidar-based statistical models derived from airborne lidar metrics (Longo et al., 2020) to estimate aboveground biomass carbon density (ABCD), basal area (BA), leaf area index (LAI), and stem number density (ND). The first-guess LAD profiles were assigned a correction factor to minimise the overall uncertainty of ABCD, BA, LAI and ND (Longo et al., 2020).

Because the airborne lidar campaign did not survey deforested areas (Ometto et al., 2023), we complemented the lidar profiles with additional patches that accounted for deforested areas. For simplicity, we assumed that these areas were pastures entirely covered with C4 grasses, and further assumed an LAI of 2m2 m−2, based on values typically found in the Amazon (Zanchi et al., 2009).

To account for the associations between forest structure and soil properties, we assigned each patch to a set of soil depth (derived from Pelletier et al., 2016), soil colour (Lawrence et al., 2007) and other soil characteristics from SoilGrids250m version 2.0 (Poggio et al., 2021). For each grid cell, we defined up to four sets of soil characteristics, which became sites, and assigned patches to each of the sites based on the similarity of soil characteristics.