The code in this repository reproduces the analysis presented in Heilmayr, Dudney and Moore, 2023 (https://www.science.org/doi/10.1126/science.adi1071)

Data download

Pre-processed data can be downloaded from the Harvard Dataverse: https://doi.org/10.7910/DVN/DZEXQN

Analysis

Once data have been downloaded, the "Full_analysis.R" provides a full walkthrough of the integrated analysis.

Outline of analysis

Environment configuration

• "0. init.R" - creates symbolic link to point towards file directory

1. Parse and detrend ITRDB data

• "1a. Pull ITRDB.R" - Pulls ITRDB files from NOAA ftp
• "1b. Parse ITRDB.R" - Reads each rwl file, detrends series, and combines into master dendro file
• "1c. Parse Klesse.R" - Reads FIA rw data from Klesse et al., 2018. Note that input data is confidential and can't be provided publicly

2. Prep climate data

• "2a. Pull site topography.R" - Extracts aspect, slope and elevation from ASTER data
• "2b. Pull site weather.R" - Extracts and downscales precip and temp history for each site
• "2c. Calculate site CWD.R" - Combines topography, swc and weather to calculate annual CWD / AET history for each site
• "2d. Historic cwdraster.R" - Calculates historic CWD / AET rasters using CRU data
• "2e. CMIP5 projections.R" - Calculates future CWD / AET rasters using CMIP5 data

3. Calculate species niches

• "3a. Collate ranges.R" - Combine individual species range maps into master file
• "3b. Species niche.R" - Calculate historic weather niche for each species. Apply species-level standardization to past and future weather and climate data

4. First stage regressions

• "4a. First stage.R" - Runs weather sensitivity regressions for each site
• "4b. DNLM first stage.R" - Re-runs first stage using dnlm model which is used as a robustness check

5. Second stage regressions

• "5a. Second stage.R" - Analyzes heterogeneity in site-level weather sensitivity across historic climate
• "5b. Robustness.R" - Runs robustness checks on second stage regressions

6. Prediction

• "6. Prediction.R" - Predicts sensitivity and RWI changes

7. Generate figures

• "7. Figure XX.R" - Generate the individual figures in the paper and SI

8. Generate tables and stats

• "8a. Table S1.R" - Generate supplementary table 1
• "8b. Paper stats.R" - Calculate all statistics reported in paper
• "8c. Missing data.R" - Track missing data

Helper functions

• "f_cwd_function.R" - Functions to process monthly weather and soil data to generate annual PET, CWD and AET.
• "f_spec_chart_function.R" - Function to run specification chart for robustness results