AZ Carbon Stores Data Comparison

This is a research compendium for a NASA CMS proposal comparing estimates of above-ground biomass in Arizona from different data products. This is a collaboration between CCT-Data Science and the David Moore lab at University of Arizona.

Reproducibility

renv

This project uses renv for package management. When opening this repo as an RStudio Project for the first time, renv should automatically install itself and prompt you to run renv::restore() to install all package dependencies.

targets

This project uses the targets package for workflow management. Run targets::tar_make() from the console to run the workflow and reproduce all results. The graph below shows the workflow:

Loading required namespace: terra

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File structure

r fs::dir_tree(recurse = 1)

.
├── LICENSE
├── R
│   ├── calc_summary.R
│   ├── crop_srer.R
│   ├── extract_agb_site.R
│   ├── get_esa_crs.R
│   ├── get_site_locs.R
│   ├── make_agb_stack.R
│   ├── make_az_sf.R
│   ├── make_ca_az_sf.R
│   ├── make_shape_list.R
│   ├── pivot_sites.R
│   ├── plot_agb_map.R
│   ├── plot_agb_ridges.R
│   ├── plot_median_map.R
│   ├── plot_scatter.R
│   ├── plot_sd_map.R
│   ├── project_crop_esa.R
│   ├── read_clean_chopping.R
│   ├── read_clean_esa.R
│   ├── read_clean_gedi.R
│   ├── read_clean_liu.R
│   ├── read_clean_lt_gnn.R
│   ├── read_clean_menlove.R
│   ├── read_clean_rap.R
│   ├── read_clean_xu.R
│   ├── trim_image.R
│   └── zip_plots.R
├── README.md
├── README.qmd
├── README.rmarkdown
├── SW_Biomass.Rproj
├── _targets
│   ├── meta
│   ├── objects
│   ├── scratch
│   └── user
├── _targets.R
├── _targets_packages.R
├── data
│   ├── rasters
│   └── shapefiles
├── docs
│   ├── fig
│   ├── report.html
│   ├── report.qmd
│   ├── report_files
│   ├── site_data.csv
│   └── xu_trend.png
├── notes
│   ├── NEON_data.png
│   ├── ameriflux.R
│   ├── estimate_file_sizes.R
│   ├── improve ridges.R
│   ├── kernel_estimation.R
│   ├── mosaic_tiles.R
│   ├── neon_usfs_data.R
│   ├── plot_doy_trends.R
│   ├── pointdensity_plots.R
│   ├── scaled_sd.R
│   ├── srer_map.R
│   └── violin_plots.R
├── renv
│   ├── activate.R
│   ├── library
│   ├── settings.json
│   └── staging
├── renv.lock
└── sync_data.R

• R/ contains functions used in the targets pipeline.
• _targets is generated by targets::tar_make() and only the metadata of the targets pipeline is on GitHub.
• _targets.R defines a targets workflow
• data/rasters is where data files for each of the data products should be placed in order to reproduce this workflow. More detailed instructions on what files are there TBD.
• data/shapefiles contains shapefiles.
• docs/ contains output figures and reports that are rendered.
• notes/ contains scripts with “sketches” about how to do things
• renv and renv.lock are necessary for the renv package to work (see above)
• _targets_packages.R is generated by targets::tar_renv() and allow renv to capture pipeline dependencies
• sync_data.R has some example code for figuring out which raw data files are actually currently used by the pipeline and syncing them to remote servers