https://github.com/tyson-swetnam/emsi
ecosystem moisture stress index
https://github.com/tyson-swetnam/emsi
data google-earth-engine javascript python rmarkdown
Last synced: 27 days ago
JSON representation
ecosystem moisture stress index
- Host: GitHub
- URL: https://github.com/tyson-swetnam/emsi
- Owner: tyson-swetnam
- License: gpl-3.0
- Created: 2018-01-07T03:06:14.000Z (almost 8 years ago)
- Default Branch: main
- Last Pushed: 2022-05-13T15:49:43.000Z (over 3 years ago)
- Last Synced: 2025-09-18T14:50:45.274Z (30 days ago)
- Topics: data, google-earth-engine, javascript, python, rmarkdown
- Language: HTML
- Homepage: https://tyson-swetnam.github.io/emsi
- Size: 107 MB
- Stars: 7
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://www.repostatus.org/#wip) [](https://opensource.org/licenses/GPL-3.0) [](https://doi.org/10.5281/zenodo.4648947)
# EMSI (Ecosystem Moisture Stress Index)
Code, example data, and manuscript supplemental materials which accompany **Swetnam, T.L.; Yool, S.R.; Roy, S.; Falk, D.A. On the Use of Standardized Multi-Temporal Indices for Monitoring Disturbance and Ecosystem Moisture Stress across Multiple Earth Observation Systems in the Google Earth Engine. Remote Sens. 2021, 13, 1448. https://doi.org/10.3390/rs13081448**
Lead Author: [Tyson Lee Swetnam](http://tyson-swetnam.github.io/) [](http://orcid.org/0000-0002-6639-7181)
Co-Authors: [Donald A. Falk](https://snre.arizona.edu/people/donald-falk) [](http://orcid.org/0000-0003-3873-722X), [Samapriya Roy](https://samapriya.github.io/) [](https://orcid.org/0000-0002-1527-2602), & Stephen Yool.
## Contents
The repository is organized (in the attempt) to enable reproducible research as part of the [FAIR data principles](https://www.go-fair.org/fair-principles/).
You can (re)run these analyses using your own computer, on commercial cloud, or a data science workbench [CyVerse](https://cyverse.org) Discovery Environment.
See our [Wiki](https://github.com/tyson-swetnam/emsi/wiki) for additional details on the background for this work.
Clone the repo to your local or VM:
```
git clone https://github.com/tyson-swetnam/emsi
```
```
gh repo clone tyson-swetnam/emsi
```
### /data
Tabular time series data presented in the manuscript.
Raster data are from [NASA data archive](https://earthdata.nasa.gov/earth-observation-data) services (e.g., [landsat](https://landsat.gsfc.nasa.gov/data/), [modis](https://modis.gsfc.nasa.gov/data/)) and ESA data services. Data are also hosted as [Google Earth Engine Collections](https://developers.google.com/earth-engine/datasets/). These raster data can be extracted to your local computer using our example `/python/*.py` scripting and `/rmd/*.Rmd` notebooks.
Previously extracted data are stored as `.csv` and geotiff `.tif` files on [CyVerse Data Store](https://data.cyverse.org/dav-anon/tswetnam/emsi), and R Markdown notebooks are provided in this repo which wil extract and render these data as the tables and figures used in the main text.
Additional derivative imagery layers from Google Earth Engine (GEE) are hosted on [CyVerse DataCommons](http://datacommons.cyverse.org/).
Original commercial imagery are available from [Planet.com](https://planet.com).
### /docker
We are hosting RStudio Server containers on CyVerse for reproducing the Rmd figures.
Dockerfiles w/ automated container builds hosted on [](https://hub.docker.com/r/cyversevice/rstudio-geospatial) [](https://circleci.com/gh/cyverse-vice/rstudio-geospatial) [](https://doi.org/10.5281/zenodo.4527797)
Container can be run on [CyVerse Discovery Environment](https://sonora.cyverse.org) 
Other CyVerse VICE images: https://github.com/cyverse-vice
### /ipynb
Notebooks (Python3) for data analyses and extraction with GEE & Planet Labs enabled Jupyter Notebooks.
### /javascripts
The JavaScript code used within [Earth Engine Code UI](https://code.earthengine.google.com/) for the intial time series point extractions, cloud-free NDVI calculations, and EMSI calculations within GEE. The [EMSI utils code repo could be found here](https://code.earthengine.google.com/?accept_repo=users/samapriya/emsi-utils) once added it should appear in your reader repositories. This contains code to generate a multiband EMSI product and to then generate a video from the multiband imagery.
You can also clone the repo scripts for Earth Engine directly by running:
```
git clone https://earthengine.googlesource.com/users/tswetnam/emsi
```
Calculate and export EMSI time series videos from GEE:
```
git clone https://earthengine.googlesource.com/users/samapriya/emsi-utils
```
### /rmd
R Markdown files with statistical data analyses for figures in manuscript.
These Rmd are also hosted as HTML on the CyVerse Data Store
[Okavango Delta example](https://data.cyverse.org/dav-anon/iplant/home/tswetnam/emsi/rmd/okavango-rasters-analyses.html)
[US-Mexico Border grasslands example](https://data.cyverse.org/dav-anon/iplant/home/tswetnam/emsi/rmd/usmex-rasters-analyses.html)
[Acre Rainforest example](https://data.cyverse.org/dav-anon/iplant/home/tswetnam/emsi/rmd/acre-rasters-analyses.html)
[Yakutia Taiga Forest example](https://data.cyverse.org/dav-anon/iplant/home/tswetnam/emsi/rmd/yakutia-rasters-analyses.html)
### /python
Python `.py` files for extracting image collections to Google Drive.