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README.md

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target-PrestoGP A targets pipeline for demonstrating the use of PrestoGP

General Steps

  1. Prepare Apptainer image
  • Replace the export directory path in the command below. This directory should be set correctly in run_apptainer.sh as well.
. ./build_apptainer_image.sh /ddn/gs1/group/set/pipeline
  • The command above will build an Apptainer image named pipeline_image.Singularity Image File (sif) named pipeline_image.sif in the specified path is built. You could run a container using the SIF file where all required packages to run the pipeline are installed. If there is no file named pipeline_image.sif in the directory, the script builds a SIF file automatically. Otherwise, it will prompt a warning message whether to overwrite the existing SIF file, then you could proceed by typing N.
  • To run the pipeline with the built image, run in SSH to NIEHS HPC
    • All paths are adjusted to point the internal paths in the Apptainer image
    • Progress is recorded in SLURM log file named pesticides_pipeline_appt.log in the working directory.
sbatch run_apptainer.sh
  1. Merge Calculated Covariates
  2. Exploratory Analysis of Covariates
  • Maps of Covariates
  • Histograms
  • Correlation Matrix
  1. Merge Covariates
  2. Save covariates as qs or fst file
  3. Run PrestoGP
  • Subset Test Locally
  • geo cluster setup
  • Run PrestoGP on geo cluster
  • Spatiotemporal Cross-Validation (branches)
  • Model Selection
  1. Save PrestoGP Results
  2. Exploratory Analysis of PrestoGP Results
  • Maps of PrestoGP Results
  • Histograms
  • Correlation Matrix
  1. Post-Processing of PrestoGP Results
  • Data Formats for sharing
  • Areal Summarization
  • Visualization

Side Option

  1. Make PrestoGP into a parsnip model