Repository restructuring -- combining with PrestoGP_Pesticides

[sigmafelix]

This repository is structured for a R package. I think the existing PrestoGP_Pesticide repository needs to be integrated into a part of this repository for both the ease of maintenance and the integration of an effective demonstration of the functions of PrestoGP. After a discussion with Kyle, we suggest taking this directory structure:

PrestoGP

• Standard R package components: included in the package build and submission to CRAN
  • ./R: R functions
  • ./data: a small subset of pesticide analysis data (e.g., data in NC), possibly in addition to the current US_ST_NO2_Data in PrestoGP package.
  • ./man: *.Rd files, generated from roxygen2
  • ./src: C++ source codes and Makevars.
  • ./tests: testthat tests, which are executable for GitHub Action test-coverage workflow
  • ./vignettes: demonstration R markdown files for PrestoGP model classes (SpatialModel, SpatioTemporalModel, MultivariateVecchiaModel, etc.) using files in ./data
• For manuscript/paper
  • ./Pesticide_Analysis: analysis codes for pesticide modeling
    • ./Pesticide_Analysis/code: similar to code folder in PrestoGP_Pesticides repository; R, rmd, qmd files are organized as follows
      • ./Pesticide_Analysis/code/00_Load_Packages
      • ./Pesticide_Analysis/code/01_Create_Dataset
      • ./Pesticide_Analysis/code/02_Geographic_Covariates
      • ./Pesticide_Analysis/code/03_Model_Fitting_and_Prediction
    • ./Pesticide_Analysis/input: shareable input data. Potentially pointing to the external websites and repository
    • ./Pesticide_Analysis/output: thematic/cleaned covariates and outcomes for model fitting and prediction

TODO

• Insang: make a new branch for implementing the directory structure