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

General Steps

0. 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

3. Merge Covariates
4. Save covariates as qs or fst file
5. Run PrestoGP

• Subset Test Locally
• geo cluster setup
• Run PrestoGP on geo cluster
• Spatiotemporal Cross-Validation (branches)
• Model Selection

6. Save PrestoGP Results
7. Exploratory Analysis of PrestoGP Results

• Maps of PrestoGP Results
• Histograms
• Correlation Matrix

8. Post-Processing of PrestoGP Results

• Data Formats for sharing
• Areal Summarization
• Visualization

Side Option

1. Make PrestoGP into a parsnip model