The Equilibrium Theory of Biodiversity Dynamics: a general framework for scaling species richness and community abundance along environmental gradients

This repository contains code to reproduce figures and some results associated with the manuscript “The Equilibrium Theory of Biodiversity Dynamics: a general framework for scaling species richness and community abundance along environmental gradients”. The statistical analyses require the function 'fit' from the Curve Fitting Toolbox (R2018 and later). The rest of the MATLAB scripts in this repository use only base MATLAB install modules and were written using release R2021a, but are expected to work on more recent releases of Matlab. In order to properly run the Matlab scripts producing the figures and statistical results, the folder <Figure> and all its contents should be added to the Matlab search path. Guide for producing figures and table contentFigure 2:Figure 2 can be reproduced by running Matlab script <figure2.m>, making sure to follow the directions in the script.Figure 3:Figure 3 can be reproduced by running Matlab script <figure3.m>, making sure to follow the directions in the script.Figure 4:Figure 4 can be reproduced by running Matlab script <figure4andfiguresS1.m>, making sure to follow the directions in the script.Figure 5:Figure 5 can be reproduced by running Matlab script <figure5andtables.m>, making sure to follow the directions in the script.Figure S1:Figure S1 can be reproduced by running Matlab script < figure4andfigureS1.m>, making sure to follow the directions in the script.Table 2: The contents for Table 2 can be reproduced by running Matlab script < figure5andtables.m>, making sure to follow the directions in the script.Table S1:The contents for Table S1 can be reproduced by running Matlab script <tableS1.m>, making sure to follow the directions in the script.Table S2:The contents for Table S2 can be reproduced by running Matlab script <tableS2.m>, making sure to follow the directions in the script.Table S3:Table S3 can be reproduced by running Matlab script < figure5andtables.m>, making sure to follow the directions in the script. List of Folders and FilesFolder: figuresFiles:delta_powerJ_full.m - function used to calculate equilibrium richness and community abundance assuming a same-abundance species abundance distribution and the full speciation and extinction functionsdelta_powerJ_powerextspec.m - function used to calculate equilibrium richness and community abundance assuming a same-abundance species abundance distribution and the power law approximations for the speciation and extinction functions lognormal_powerJ_full.m - function used to calculate equilibrium richness and community abundance assuming a lognormal species abundance distribution and the full speciation and extinction functionsrma_jgo.m - function used to calculate the reduced major axis regression model parameters from datarma_plot.m - function used to calculate the reduced major axis regression model parameters from data and plot the data and regression modelfigure2.m - produces the basic version of figure 2figure3.m - produces the basic version of figure 3figure4andfigureS1.m - produces the basic version of figure 4 and figure S1figure5andtables.m - produces the basic version of figure 5 and the statistics used to produce table 2tableS1.m - produces the statistics used to produce tables S1tableS2.m - produces the statistics used to produce tables S1-1.txt - the plot-level 0.1-1 sq km data from Keil and Chase (2019) used by tableS1.m-1_cleaned.txt - the plot-level 0.1-1 sq km data from Keil and Chase (2019) used by figure5andtables.m-2.txt - the plot-level 0.01-0.1 sq km data from Keil and Chase (2019) used by tableS1.m-2_cleaned.txt - the plot-level 0.01-0.1 sq km data from Keil and Chase (2019) used by figure5andtables.mCountries_localregional_norm.txt - the estimates of species richness per 100,000 sq km for each biome, used by figure5andtables.m and tableS1.m, along with the country level data from Keil and Chase (2019)joint.txt - array used by tableS1.mjoint2.txt - array used by tableS1.mjoint2_norm_take2.txt - array used by figure5andtables.mjoint_norm.txt - array used by figure5andtables.m Folder: dataFiles:Plots_data_KeilChaseSubset - the plot-level data used from Keil and Chase (2019). See Keil and Chase (2019) for metadata.Country_KeilChaseSubset - the country-level data used from Keil and Chase (2019). See Keil and Chase (2019) for metadata. ReferencesKeil, P., and J. M. Chase. 2019. Global patterns and drivers of tree diversity integrated across a continuum of spatial grains. Nature ecology & evolution 3:390–399.