README Document for Amazon_MEWS_LDAS Repository

Created March 2022 by Tashiana Osborne - JHU
Last Modified March 2022 by T. Osborne

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KEY ACRONYMS
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  JHU:    Johns Hopkins University (Baltimore, MD, USA)
  LDAS:   Land Data Assimilation System
  LISF:   Land Information System Framework (the LDAS is run within this 3-component system)
           (1) LDT: Land surface Data Toolkit
           (2) LIS: LIS Core; main component of LISF (where LDAS is ran)
           (3) LVT: Land surface Verification Toolkit
  MEWS:   Malaria Early Warning System 
  NASA:   The National Aeronautics and Space Administration
  USFQ:   Universidad San Francisco de Quito (Quito, Ecuador)
  WTSA:   Western Tropical South America

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PROJECT DESCRIPTION: LDAS FOR AMAZON MEWS 
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NASA LISF (which contains a Land Data Assimilation System - LDAS) is employed here as part of the 
Malaria Early Warning System (MEWS) for the Amazon Rainforest region. 

This project is an interdisciplinary (geosciences and epidemiology), international, and multi-institutional
collaboration between researchers at the Universidad San Francisco de Quito, Duke University, Johns Hopkins 
University, and others focused on the Amazon and/or Western Tropical region of South America. 

Broadly, the MEWS project investigates and makes predictions of meteorological, hydrological, land surface, 
epidemiological and public health, and societal variables and factors that affect malaria risk in the Amazon. 
Additional foci and factors can also be considered as LIS can be applied to numerous science-societal or 
science-to-action goals. Materials within this repository are intended to be used as a base on which to 
build or to apply the LDAS (within LISF) to various projects.

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WHAT IS INCLUDED IN THIS REPOSITORY
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(1) Scripts for data extraction, analysis, and post-processing of LDAS output (primarily Python and MATLAB)
(2) New User Startup Guide for LDAS (originally created for USFQ and Collaborators for Dec 2021 Workshop)
(3) Input LIS and LDT configuration files (.config) used to run the LDAS within LIS
(4) Possible Inclusion in the Future: Scripts from researchers at Duke University (Mark Janko, Willian Pan, and others) to process LDAS output for 
    use as input for epidemiological statistic models


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USE OF SCRIPTS AND OTHER MATERIAL 
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Authors of works included in this repository intend for materials to be open-source and easily accessible for others who are interested in using LISF.
Please refer to the LICENSE document (osbornesci/Amazon_MEWS_LDAS/LICENSE) for details on usage of materials. 

(If the LICENSE document is not yet available, it will be included in the future. Please email [email protected] if this is the case and you are 
interested in using any of the materials currently existing within this repository.)


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ADDITIONAL INFORMATION AND RESOURCES
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    - LISF and applications: https://lis.gsfc.nasa.gov 
    - LIS discussion board (Q&A on finer details of LIS): https://github.com/NASA-LIS/LISF/discussions
    - Archived LDT and LIS config files and corresponding output from simulations performed with the Noah-MP LSM and HyMAP 
      (Amazon region, Jan. 2002 - Sep. 2019), courtesy of Cristina Recalde: https://archive.data.jhu.edu/dataset.xhtml?persistentId=doi:10.7281/T1/YQDI0F 
    - Options for LIS Framework config files (namelist options):
      * ldt.config README: https://github.com/NASA-LIS/LISF/blob/master/ldt/configs/ldt.config.adoc
      * lis.config README: https://github.com/NASA-LIS/LISF/blob/master/lis/configs/lis.config.adoc 
    - Source code for LDT component: https://github.com/NASA-LIS/LISF/tree/master/ldt/core (fortran; note modularity - processes are separated into modules)
    - Source code for LIS component: https://github.com/NASA-LIS/LISF/tree/master/lis/core 
    - Quick intro to ncview: http://cirrus.ucsd.edu/~pierce/software/ncview/quick_intro.html  

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REFERENCES
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NASA LIS -- Kumar, S.V., C.D. Peters-Lidard, Y. Tian, P.R. Houser, J. Geiger, S. Olden, L. Lighty, J.L. Eastman, B. Doty, P. Dirmeyer, J. Adams, K. Mitchell, 
E.F. Wood, and J. Sheffield, 2006: Land Information System - An interoperable framework for high resolution land surface modeling. Environ. 
Modeling & Software, 21, 1402-1415, https://doi.org/10.1016/j.envsoft.2005.07.004.

Archived LDAS Output for Amazon Region -- Recalde, C., B.F. Zaitchik, and W.K. Pan, 2021: Data associated with: Retrospective land surface model simulations of 
Western Tropical South America (WTSA), https://doi.org/10.7281/T1/YQDI0F, Johns Hopkins University Data Archive, V1.

Additional NASA LIS Publications -- https://lis.gsfc.nasa.gov/publications