MPM Sampling Uncertainty

Data and code for analyses of sampling uncertainty in published projection matrices.

This repository is organized to support replicability and FAIR principles. The main analysis workflow lives in scripts/, reusable functions in code/, models in models/, and data split into data/raw/ (as obtained) and data/derived/ (processed/intermediate).

Quick start

• Run scripts/00_check_setup.R to verify packages and required inputs.
• Start with scripts/ in numeric order (S01 ... S14). Each script is intended to be run after prior steps.
• Outputs that are reused across scripts are cached under data/derived/analysis_cache/.
• Figures are written to figures/ with filenames set in the scripts.

Data sources

• COMPADRE: canonical snapshot v6.26.3.0 plus a project-specific corrected copy generated by scripts/S01_compadre_correct.R (recorded in data/metadata/sources.md).
• Ellis et al. (2012) supplemental matrices.
• PRISM climate rasters are downloaded via prism configured by setup_prism() in code/setup.R, used in scripts/S11_case_study_2_prism.R, which writes to data/raw/prism/ and should run before scripts/S12_case_study_2.R for analysis 2.

Folder guide

• code/ Reusable R functions used by multiple scripts.
• scripts/ Analysis scripts (numbered, run in order).
• models/ Stan model definitions.
• data/raw/ Raw source data, as obtained from external sources.
• data/derived/ Processed data and intermediate analysis artifacts.
• data/metadata/ Data dictionaries and provenance notes.
• figures/ Generated figures for the paper.
• docs/ Notes, methods, and documentation.
• docs/manuscript/ Main manuscript and supplement Rmd files, render scripts, and submission materials.

Notes

• Some external data sources require download (e.g., PRISM rasters). Use the prism R package workflow in scripts/S11_case_study_2_prism.R which stores files under data/raw/prism/ (ignored by git). See data/metadata/.