Some Biodiversity Covariates

This repository contains scripts to download (or remotely access) globally available covariates to help scale biodiversity predictions from https://github.com/gjearevoll/BioDivMapping.

For now (testing phase), soil properties and canopy height for Trøndelag region is provided.

Overview

• SoilGrids (Website, Viewer, Paper 1, Paper 2, Paper 3, Data Help, Data)
• ETH Canopy Height (Website, Viewer, Paper, Data Help, Data)
• CCI Land Evaporation (Website)

Prerequisites

0. Install uv from https://docs.astral.sh/uv/.
1. Sync packages

$ uv sync

Soilgrids

Run as

$ uv run soilgrids_trondelag.py

This generates the following files (in soilgrids_trondelag_output)

File	Variable	Unit	Depth
bdod_0-5cm_mean_trondelag_utm33n.tif	Bulk Density	cg/cm3	0-5cm
cec_0-5cm_mean_trondelag_utm33n.tif	Cation Exchange Capacity at pH7	mmol(c)/kg	0-5cm
cfvo_0-5cm_mean_trondelag_utm33n.tif	Coarse Fragments Volume	cm3/dm3	0-5cm
clay_0-5cm_mean_trondelag_utm33n.tif	Clay Content	g/kg	0-5cm
nitrogen_0-5cm_mean_trondelag_utm33n.tif	Nitrogen Content	cg/kg	0-5cm
ocd_0-5cm_mean_trondelag_utm33n.tif	Organic Carbon Density	hg/m3	0-5cm
ocs_0-30cm_mean_trondelag_utm33n.tif	Organic Carbon Stock	t/ha	0-30cm
phh2o_0-5cm_mean_trondelag_utm33n.tif	pH in Water	ph*10	0-5cm
sand_0-5cm_mean_trondelag_utm33n.tif	Sand	g/kg	0-5cm
silt_0-5cm_mean_trondelag_utm33n.tif	Silt	g/kg	0-5cm
soc_0-5cm_mean_trondelag_utm33n.tif	Soil Organic Carbon	dg/kg	0-5cm

See also https://docs.isric.org/globaldata/soilgrids/SoilGrids_faqs_01.html#sec-faq2.

ETH Canopy Height

First, download tiles containing Trøndelag

$ ./canopy_trondelag_download_tiles.sh

Then clip to Trøndelag boundary

$ uv run canopy_trondelag_local.py

This generates the file canopy_trondelag_output/canopy_height_trondelag_10m.tif

You can also use canopy_trondelag.py which runs on the (remotely) hosted global raster, but it's very slow to avoid being rate limited.

CCI Land Evaporation

This is a pre-production dataset and not publicly available yet. We will update the scripts once it is.

First, download files from the FTP server into the following directory structure

$ tree -L 3 data
data
└── cci-evaporation
    └── yearly
        ├── E
        ├── Eb
        ├── Ec
        ├── Ei
        ├── Ep
        ├── Es
        ├── Et
        ├── Ew
        ├── H
        ├── S
        ├── SMrz
        └── SMs

Then, from the root of this repository, run

$ ./evaporation.sh

This will produce the following structure

$ tree -L 3 output/cci-evaporation
output/cci-evaporation
└── trondelag
    ├── E_trondelag_mean.tif
    ├── Eb_trondelag_mean.tif
    ├── Ec_trondelag_mean.tif
    ├── Ei_trondelag_mean.tif
    ├── Ep_trondelag_mean.tif
    ├── Es_trondelag_mean.tif
    ├── Et_trondelag_mean.tif
    ├── Ew_trondelag_mean.tif
    ├── H_trondelag_mean.tif
    ├── S_trondelag_mean.tif
    ├── SMrz_trondelag_mean.tif
    └── SMs_trondelag_mean.tif

Where files contain the following variables

File	Variable	Unit
E_trondelag_mean.tif	Actual evaporation	mm/yr
Eb_trondelag_mean.tif	Bare soil evaporation	mm/yr
Ec_trondelag_mean.tif	Condensation	mm/yr
Ei_trondelag_mean.tif	Interception loss	mm/yr
Ep_trondelag_mean.tif	Potential evaporation	mm/yr
Es_trondelag_mean.tif	Snow sublimation	mm/yr
Et_trondelag_mean.tif	Transpiration	mm/yr
H_trondelag_mean.tif	Sensible heat flux	W/m2
S_trondelag_mean.tif	Evaporative stress	-
SMrz_trondelag_mean.tif	Root-zone soil moisture	m3/m3
SMs_trondelag_mean.tif	Surface soil moisture	m3/m3

Variables are averaged over the yearly values from 1980 to 2025.

Contact

• Volker Hoffmann (volker.hoffmann@sintef.no)