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pods

Python

  1. Download Sentinel-2 data from Digital Earth Africa (DEA) using the DEA Sandbox and S2_download_git.ipynb. Data exported to .tif files.
  2. Download VIIRS Land Cover Dynamics (LCD) data from Google Earth Engine (GEE) using extract_gee_coll_LCD_download.ipynb. Data exported to .csv files for each year.
  3. Export VIIRS surface reflectance data from GEE using extract_gee_coll_VIIRS.ipynb. Data is exported to.csv files.
  4. Download Sentinel-1 data from GEE using extract_gee_coll_s1_download.ipynb. Perform guided filter using sentinel_1_guided_filter.ipynb.
  5. **(needs review) Join data for Mark sensors and VIIRS surface reflectance using join_pods_VIIRS.ipynb. Data is saved to all_joined.csv.

R

  1. Use 'pre_analysis_remove_secondary_S1.R' to filter the ascending orbit images to the most common view angle.
  2. 'Analysis_PRE_PROCESSING.Rmd' performs several pre-processing steps, including joining Sentinel-1 and 2 data, splitting Kenya data into separate seasons, and calculating VI dormancy values.
  3. 'Analysis_PHENO_FITTING.Rmd' performs padding for Mark time-series, masking for Sentinel-2 and VIIRS surface reflectance, and curve-fitting and Land Surface Phenology (LSP) extraction for Mark, Sentinel 1 and 2, VIIRS surface reflectance, and VIIRS Land Cover Dynamics (LCD). It also joins management data (planting and harvest) to site table.
  4. 'Analysis_QUALITYCHECK.Rmd' outputs a pdf for visual interpretation to assess Mark LSP dates. After interpreting, Mark LSP dates that are not considered valid are excluded form downstream tasks.
  5. 'Analysis_MULTISENSOR.Rmd' calculates mean and median LSP values, and uses a random forest model to calculate LSP dates, excluding each site's current group from training the model.
  6. 'Analysis_PAPER_TABLES_PLOTS.Rmd' performs agreement analysis (bias, MAD, R-squared) used in paper figures and tables. Outputs are labeled with Table/Figure number in final paper.
  7. ''Analysis_FIGURES.Rmd' creates two visual diagrams (workflow and full-season length comparison) used in paper. The output figures are labeled with their Figure number in final paper.

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