Skip to content

Latest commit

 

History

History
33 lines (23 loc) · 2.78 KB

README.md

File metadata and controls

33 lines (23 loc) · 2.78 KB
Raw

Earth_obs_cleaning is an R- and Docker-based tool to predict the difference between AERONET and MCD19A2 satellite aerosol optical depth (AOD), and apply such predictions to improve the same AOD product.

Installation

A high-end machine may be required for running large workflows, but shouldn't be necessary for the test workflow described in the following section.

  1. Create a data directory. The data directory will store code, downloaded data, cached results, and temporary files. For large workflows, expect terabytes of stuff to go into it.
  2. Create a configuration file named config.yaml in the data directory. See the directory example in the Earth_obs_cleaning repository for examples.
  3. Clone this repository to the data directory, and name the new directory src. (Actually, of the items in this repository, only renv.lock, code, and writing are required.)
  4. To build the Docker image, use the command docker build --tag=earth_obs_cleaning .
  5. To use the image to create a container and start R interactively, say docker run --rm -it --mount type=bind,src=DPATH,target=/data -e EARTHDATA_USERNAME -e EARTHDATA_PASSWORD earth_obs_cleaning
    • Replace DPATH with the path to your data directory.
    • Notice that the environment variables EARTHDATA_USERNAME and EARTHDATA_PASSWORD should be set in your real environment; these are NASA Earthdata login credentials for downloading satellite data.
    • --rm is used to automatically delete the container after the R process exits. This is convenient but not necessary.
  6. In R, say:
    • renv::init()
      • 1
    • unlink(".Rprofile")
    • cat("TRUE\n", file = "/data/R-packages-installed")

Usage

Run a Docker container as described above in step 5 above. (If you installed renv packages in this R session, quit and restart.) You can now use tar_make to build targets.

To run the test workflow, ensure test.small.daterange in the configuration file is TRUE. Then say tar_make(cv) to try cross-validation with a few days of data. This is pretty fast, taking only a few minutes, aside from downloading the data. Use tar_read (as in tar_read(cv)) to see the results.

License

This program is copyright 2019–2024 Kodi B. Arfer, Allan C. Just, Yang Liu, and Johnathan Rush.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.