README.qmd

---
format: gfm
---

# Assessing the performance of spatial cross-validation approaches for models of spatially structured data

This repository contains the code and files necessary to create the paper "[Assessing the performance of spatial cross-validation approaches for models of spatially structured data](./paper_outputs/spatial_cv_arxiv.pdf)", hopefully published in 2023. 

The project is structured to use the [targets](https://books.ropensci.org/targets/) package. You can reconstruct any step of the project via `targets::tar_make()`. Note that the simulations will take a few weeks to run on a standard computer.

The paper itself is a [Quarto](https://quarto.org/) document, saved as the [paper.qmd](./paper.qmd) file. 

This repository is structured as follows:

```
.
|
|__ R/ # Scripts and functions for processing and visualization
  |
  |_ calculate_autocorrelation_range.R # Empirical variograms
  |
  |_ calculate_block_resamples.R # Spatial blocking RMSE values
  |
  |_ calculate_clustered_resamples.R # Spatial clustering RMSE values
  |
  |_  calculate_ideal.R  # "True" RMSE values
  |
  |_ calculate_leave_disc_out_resamples.R # LODO & BLO3 RMSE values
  |
  |_ calculate_random_resamples.R # V-fold CV RMSE values
  |
  |_ calculate_target.R # 5th and 95th percentile of "true" RMSE
  |
  |_ calculate_training.R # Apparent RMSE values
  |
  |_ combine_rmse_tables.R # Combine RMSE values into one table
  |
  |_ create_rf_workflow.R # Random forest "workflow" creation
  |
  |_ create_sims.R # Landscape simulation from Roberts et al. (2017)
  |
  |_ discrete_colors.R # Color scale for most graphs
  |
  |_ plot_maps.R # Figure 1 function
  |
  |_ proportion_all_runs_in_good.R # % of runs within ideal RMSE calculation
  |
  |_ theme_pub.R # ggplot2 theme for graphs
|
|_ _extensions/mikemahoney218/arxiv/ # Quarto format for the preprint
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|_ _freeze/paper/ # Cached outputs from previous paper renders
|
|_ _targets/ # Data and metadata from the targets pipeline
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|_ paper_outputs/
  |
  |_ paper_files/figure-pdf/ # Figures for the PDF output
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  |_ spatial_cv_arxiv.pdf/ # The rendered PDF version of the paper
|
|_ .gitignore # File controlling git behavior
|
|_ _quarto.yml # Metadata file for Quarto rendering
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|_ _targets.R # Script controlling the targets pipeline
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|_ paper.bib # The BibTeX file for references for the paper
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|_ paper.qmd # The Quarto document which creates the paper
|
|_ run.R # R script to run the targets pipeline
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|_ run.sh # Shell script to run the targets pipeline
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|_ simulated_spatialsample.Rproj # File for opening this project in RStudio
```