README added

Hunka_2023_ERL/.ipynb_checkpoints/_README-checkpoint.txt

+###############################################################################################################
+
+#### This folder provides the code associated with artcle : 
+
+# @article{10.1088/1748-9326/ad0b60,
+# author={Hunka, Neha and Santoro, Maurizio and Armston, John and Dubayah, Ralph and McRoberts, Ronald and Næsset, Erik and Quegan, Shaun and Urbazaev, Mikhail and Pascual, Adrián and May, Paul B and Minor, David and Leitold, Veronika and Basak, Paromita and Liang, Mengyu and Melo, Joana and Herold, Martin and Malága, Natalia and Wilson, Sylvia and Montesinos, Patricia Durán and Arana, Alexs and De La Cruz Paiva, Ricardo Ernesto and Ferrand, Jeremy and Keoka, Somphavy and Guerra-Hernandez, Juan and Duncanson, Laura},
+# title={On the NASA MAP and ESA CCI biomass maps: Aligning for uptake in the UNFCCC global stocktake},
+# journal={Environmental Research Letters},
+# url={http://iopscience.iop.org/article/10.1088/1748-9326/ad0b60},
+# year={2023}
+# }
+
+#### Please contact author Neha Hunka (nhunka@umd.edu) for further information 
+
+##################################################################################################################
+
+1) The DPS_Config folder provides the configuration files to batch process country-level or ecoregion-level (or any arbitrary geographic boundary) statistics from various EO maps (e.g. CCI, GEDI). It is designed to run on the NASA Multi-Mission Algorithm and Analysis Platform (MAAP), backed by AWS.  
+
+2) Country_summaries.ipynb provides one example of the above, as a Jupyter notebook, run for the country of Laos. The supporting functions are available in the file Country_summaries_functions.R. 
+
+3) DPS_run_country_summaries.ipynb provides code to submit the batch-processing of jobs described in (1), as well as a post-processing analysis of the results of the 4 countries in the study (Mexico, Peru, Spain and Laos). The results for Laos are, however, redacted due to restricted sharing of NFI data.  
+
+4) L2A_Subset.ipynb provides the use of the GEDI subsetter to extract L2A relative height metrics and L4A footprint-level AGBD estimates for any country, ecoregion or an arbitrary geographic boundary. Please cite: Chuck Daniels, Jamison French, Slesa Adhikari, Anish Bhusal, Alex, & Sheyenne Kirkland. (2023). MAAP-Project/gedi-subsetter: 0.6.1 (0.6.1). Zenodo. https://doi.org/10.5281/zenodo.10019415
+
+5) FH_ERL_paper.ipynb is the Fay-Herriot small area estimation model used to compare NFI-estimated and map-estimated AGBD. NFI_MAP_AGBD_mock.csv provides a mock dataset of NFI AGBD estimates to run the script. Please cite: Neha, H., Paul, M., & Laura, D. (2023). Comparison of NFI-based and EO-based mean forest biomass estimates: Fay-Herriot small area estimation. In Environmental Research Letters (1.0). Zenodo. https://doi.org/10.5281/zenodo.10137632
\ No newline at end of file

Hunka_2023_ERL/DPS_Config/.ipynb_checkpoints/Package_list-checkpoint.sh

+conda activate r-with-gdal
+conda install -c conda-forge r-raster --yes
+conda install -c conda-forge r-rgdal --yes
+conda install -c conda-forge r-rgeos --yes
+conda install -c conda-forge r-rColorBrewer --yes
+conda install -c conda-forge r-gdalUtils --yes
+conda install -c conda-forge r-jpeg --yes
+conda install -c conda-forge r-plyr --yes
+conda install -c conda-forge r-sf --yes
+conda install -c conda-forge r-geosphere --yes
\ No newline at end of file

Hunka_2023_ERL/DPS_Config/Package_list.sh

+conda activate r-with-gdal
+conda install -c conda-forge r-raster --yes
+conda install -c conda-forge r-rgdal --yes
+conda install -c conda-forge r-rgeos --yes
+conda install -c conda-forge r-rColorBrewer --yes
+conda install -c conda-forge r-gdalUtils --yes
+conda install -c conda-forge r-jpeg --yes
+conda install -c conda-forge r-plyr --yes
+conda install -c conda-forge r-sf --yes
+conda install -c conda-forge r-geosphere --yes
\ No newline at end of file

Hunka_2023_ERL/DPS_Config/algorithm_config.yaml

+algo_name: run_country_summaries
+version: AGB_ecoregions_PART2
+environment: ubuntu
+repository_url: https://repo.ops.maap-project.org/lduncanson/biomass_harmonization.git
+docker_url: mas.maap-project.org:5000/root/ade-base-images/r:latest
+queue: maap-dps-worker-32gb
+description: Test algo for biomass harmonization
+build_command: biomass_harmonization/country_summaries/dps/build_command_main.sh
+run_command: biomass_harmonization/country_summaries/dps/run_country_summaries.sh
+disk_space: 50GB 
+inputs:
+  - name: ISO3_code
+    download: False
+  - name: Shapefile_url 
+    download: True
+  - name: Shapefile
+    download: False
+  - name: Map_list
+    download: False
+  - name: GEDI_file_url
+    download: True
+  - name: GEDI_file
+    download: False
+  - name: NCEO_file_url
+    download: True
+  - name: NCEO_file
+    download: False
+  - name: CCI_file_url
+    download: True
+  - name: CCI_file
+    download: False
+  - name: GEDI_SE_file_url
+    download: True
+  - name: GEDI_SE_file
+    download: False
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Hunka_2023_ERL/DPS_Config/build_command_main.sh

+#!/bin/bash
+set -x
+basedir=$( cd "$(dirname "$0")" ; pwd -P )
+conda env update -n run_country_summaries --file "${basedir}/env_main.yaml"
+
+source activate r-with-gdal
+conda install -c conda-forge r-raster --yes
+conda install -c conda-forge r-rgdal --yes
+conda install -c conda-forge r-rColorBrewer --yes
+conda install -c conda-forge r-gdalUtils --yes
+conda install -c conda-forge r-jpeg --yes
+conda install -c conda-forge r-rgeos --yes
+conda install -c conda-forge r-sf --yes
+conda install -c conda-forge r-plyr --yes
+conda install -c conda-forge r-geosphere --yes
\ No newline at end of file

Hunka_2023_ERL/DPS_Config/env_main.yaml

+name: r-with-gdal
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+    - r-raster
+    - r-rgdal
+    - r-rColorBrewer
+    - r-gdalUtils
+    - r-rgeos
+    - r-jpeg
+    - r-sf
+    - r-plyr
+    - r-geosphere
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Hunka_2023_ERL/DPS_Config/run_country_summaries.sh

+#!/bin/bash
+
+source activate r-with-gdal 
+basedir=$( cd "$(dirname "$0")" ; pwd -P )
+
+mkdir output
+
+ISO3_code=${1}
+Shapefile=${2}
+Map_list=${3}
+GEDI_file=${4}
+NCEO_file=${5}
+CCI_file=${6}
+GEDI_SE_file=${7}
+
+OUTPUTDIR="${PWD}/output"
+
+Rscript ${basedir}/Country_summaries_DPS.R ${ISO3_code} ${Shapefile} ${Map_list} ${GEDI_file} ${NCEO_file} ${CCI_file} ${GEDI_SE_file}  
\ No newline at end of file

Hunka_2023_ERL/_README.txt

+###############################################################################################################
+
+#### This folder provides the code associated with artcle : 
+
+# @article{10.1088/1748-9326/ad0b60,
+# author={Hunka, Neha and Santoro, Maurizio and Armston, John and Dubayah, Ralph and McRoberts, Ronald and Næsset, Erik and Quegan, Shaun and Urbazaev, Mikhail and Pascual, Adrián and May, Paul B and Minor, David and Leitold, Veronika and Basak, Paromita and Liang, Mengyu and Melo, Joana and Herold, Martin and Malága, Natalia and Wilson, Sylvia and Montesinos, Patricia Durán and Arana, Alexs and De La Cruz Paiva, Ricardo Ernesto and Ferrand, Jeremy and Keoka, Somphavy and Guerra-Hernandez, Juan and Duncanson, Laura},
+# title={On the NASA MAP and ESA CCI biomass maps: Aligning for uptake in the UNFCCC global stocktake},
+# journal={Environmental Research Letters},
+# url={http://iopscience.iop.org/article/10.1088/1748-9326/ad0b60},
+# year={2023}
+# }
+
+#### Please contact author Neha Hunka (nhunka@umd.edu) for further information 
+
+##################################################################################################################
+
+1) The DPS_Config folder provides the configuration files to batch process country-level or ecoregion-level (or any arbitrary geographic boundary) statistics from various EO maps (e.g. CCI, GEDI). It is designed to run on the NASA Multi-Mission Algorithm and Analysis Platform (MAAP), backed by AWS.  
+
+2) Country_summaries.ipynb provides one example of the above, as a Jupyter notebook, run for the country of Laos. The supporting functions are available in the file Country_summaries_functions.R. 
+
+3) DPS_run_country_summaries.ipynb provides code to submit the batch-processing of jobs described in (1), as well as a post-processing analysis of the results of the 4 countries in the study (Mexico, Peru, Spain and Laos). The results for Laos are, however, redacted due to restricted sharing of NFI data.  
+
+4) L2A_Subset.ipynb provides the use of the GEDI subsetter to extract L2A relative height metrics and L4A footprint-level AGBD estimates for any country, ecoregion or an arbitrary geographic boundary. Please cite: Chuck Daniels, Jamison French, Slesa Adhikari, Anish Bhusal, Alex, & Sheyenne Kirkland. (2023). MAAP-Project/gedi-subsetter: 0.6.1 (0.6.1). Zenodo. https://doi.org/10.5281/zenodo.10019415
+
+5) FH_ERL_paper.ipynb is the Fay-Herriot small area estimation model used to compare NFI-estimated and map-estimated AGBD. NFI_MAP_AGBD_mock.csv provides a mock dataset of NFI AGBD estimates to run the script. Please cite: Neha, H., Paul, M., & Laura, D. (2023). Comparison of NFI-based and EO-based mean forest biomass estimates: Fay-Herriot small area estimation. In Environmental Research Letters (1.0). Zenodo. https://doi.org/10.5281/zenodo.10137632
\ No newline at end of file