README

Repository for: Wieczynski, D.J., P. Singla, A. Doan, A. Singleton, Z. Han, S. Votzke, A. Yammine, & J.P. Gibert. Linking species traits and demography to explain complex temperature responses across levels of organization. (In press, Proceedings of the National Academy of Sciences)

To access all files, download PNAS_Wieczynski_etal_2021_Master.tar.gz to your home directory and double click to open. The zip file will open automatically and all files will be available for use.

Code:

1. Main data analysis (MainAnalysis.R)
   a. Analysis of all experimental data (density dependence assays, TPC assays, and associated statistical analyses)
   b. TPC predictions using traits as inputs
   c. Import and analyze model results
   d. Generate raw figure graphics for both empirical and model results.
2. Community model (CommunityModel.nb)
   a. Calculate equilibrium densities across temperatures using both empirical and predicted TPCs while also varying model parameters.
   b. Generate community network diagrams

Data (/data):

1. Raw empirical data.
   a. Density dependence assays (Demography.csv)
   b. TPC assays (TPCs.csv).
   c. Trait measurements (Traits.csv).
   d. Community experiment (CommunityExperiment_data.csv).
2. Data generated by analysis of raw empirical data:
   a. Summary statistics for density dependence assay regressions (demo_regression_summary.csv).
   b. Demographic parameter results from density dependence assays (demo_parameters.csv).
   c. Measured TPC parameters (TPC_parameters.csv).
   d. Commonality analysis summary statistics for TPC/demographic parameter-trait regressions (param_trait_commonality_summary.csv).
3. Input data for community model.
   a. Empirical TPC parameters (TPC_model_parameters.csv).
   b. Trait-based (predicted) TPC parameters (TPC_model_parameters_est.csv).
   c. Summary of trait data (traits_summary.csv).
   d. Summary of demographic data (demo_parameters.csv).
4. Community model output data.
   a. Output from small-run model results used in Figures 5/S4 A & E-G (model_rawdata_small.csv).
   b. Output from large-run model results used in Figures 5/S4 B-D (/temp/*_model_rawdata_temp.csv).
   Note: Large runs are computationally intensive (taking several hours on a typical personal computer).

Graphics (/graphics).

1. Raw graphics outputs for figures.

Funding for this project: JPG’s Duke University startup funds and a U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program under Award Number DE-SC0020362.