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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”, hopefully published in 2023.

The project is structured to use the 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 document, saved as the paper.qmd file.

This repository is structured as follows:

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