This repo containts scripts for the simulations and analyses in "Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances", Felce et al.
The scripts for simulations, and the scripts for fitting the simulated data with the various models, are included in the simulations folder. This includes scripts for plotting the true vs estimated parameter plots and the AIC comparison plots in the supplement.
The scripts for the dN/dS analysis in the Supplementary Information and the plotting script for S5 are included in dN_dS_analysis.
The data used in the phylogenetic modeling, and the scripts for fitting the OU models to data are included in the phylogenetic_input folder. This includes the script for creating Figure 2 of the main manuscript.
The MCMC folder contains the simulation and fitting scripts used for the true vs estimated parameter plot in Supplementary Information (Figure S6). It also contains the fitting script and the plotting script used for the posterior parameter distributions for b, beta and gamma (Figures S7 & S8).
The fits for the expression-binned data, along with the script for producing Figure 3, is included in Figure_3.