sylvainschmitt / ideas

My participation into the IDEAS project. The aim is to build climate indices related to land use change in Guaviare.

IDEAS

Sylvain Schmitt - Jan 24, 2024

• Installation
• Usage
• Configuration
• Workflow
• Data
• Development

My participation into the IDEAS project - Investigación y Desarrollo para la Estabilización de la frontera Agropecuaria en Colombia. The aim is to build climate indices related to land use change in Guaviare.

Installation

This workflow is built on:

• Python ≥3.5
• Mambaforge

conda activate base
mamba create -c conda-forge -c bioconda -n snakemake snakemake
conda activate snakemake
snakemake --help

Once installed simply clone the workflow:

git clone [email protected]:sylvainschmitt/ideas.git
cd ideas
snakemake -np 

Usage

module load bioinfo/Snakemake/7.20.0 # for test on nod depending on your HPC
snakemake -np # dry run
snakemake --dag | dot -Tsvg > dag/dag.svg # dag
snakemake -j 1 --resources mem_mb=10000 # local run (test)
sbatch job_muse.sh # HPC run with slurm

Configuration

Different configuration parameters to set in config/config.yml ordered by steps:

Workflow

Step

get_chirps

• Script: get_chirps.py
• Environment: xarray.yml

Description.

Data

CHIRPS 2.0: Rainfall Estimates from Rain Gauge and Satellite Observations

Climate Hazards Group InfraRed Precipitation with Station data (CHIRPS) is a 35+ year quasi-global rainfall data set. Spanning 50°S-50°N (and all longitudes) and ranging from 1981 to near-present, CHIRPS incorporates our in-house climatology, CHPclim, 0.05° resolution satellite imagery, and in-situ station data to create gridded rainfall time series for trend analysis and seasonal drought monitoring.

TMF V2.1.1: Tracking long-term (1990-2022) deforestation and degradation in tropical moist forests

The European Commission’s Joint Research Centre developed this new dataset on forest cover change in tropical moist forests (TMF) using 41 years of Landsat time series. The wall-to-wall maps at 0.09 ha resolution (30m) depict the TMF extent and the related disturbances (deforestation and degradation), and post-deforestation recovery (or forest regrowth) through two complementary thematic layers: a transition map and an annual change collection over the period 1990-2022. Each disturbance (deforestation or degradation) is characterized by its timing and intensity. Deforestation refers to a change in land cover (from forest to non-forested land) when degradation refers to a temporary disturbance in a forest remaining forested such as selective logging, fires and unusual weather events (hurricanes, droughts, blowdown).

MODIS: Moderate Resolution Imaging Spectroradiometer

MODIS (or Moderate Resolution Imaging Spectroradiometer) is a key instrument aboard the Terra (originally known as EOS AM-1) and Aqua (originally known as EOS PM-1) satellites. Terra’s orbit around the Earth is timed so that it passes from north to south across the equator in the morning, while Aqua passes south to north over the equator in the afternoon. Terra MODIS and Aqua MODIS are viewing the entire Earth’s surface every 1 to 2 days, acquiring data in 36 spectral bands, or groups of wavelengths (see MODIS Technical Specifications). These data will improve our understanding of global dynamics and processes occurring on the land, in the oceans, and in the lower atmosphere. MODIS is playing a vital role in the development of validated, global, interactive Earth system models able to predict global change accurately enough to assist policy makers in making sound decisions concerning the protection of our environment.

ERA5-Land

ERA5-Land is a reanalysis dataset providing a consistent view of the evolution of land variables over several decades at an enhanced resolution compared to ERA5. ERA5-Land has been produced by replaying the land component of the ECMWF ERA5 climate reanalysis. Reanalysis combines model data with observations from across the world into a globally complete and consistent dataset using the laws of physics. Reanalysis produces data that goes several decades back in time, providing an accurate description of the climate of the past.

Development

First create or update the dev-ideas mamba environment with required libraries:

mamba env create -f envs/dev-ideas.yml # init
mamba env update -f envs/dev-ideas.yml --prune # update
mamab activate dev-ideas