file_desription.md

Description of scripts for simulations and plots

Simulation_1_no_exp_evo_comp_evo.R

• Simulates scenario i where expression is static, however abundance evolves under Brownian Motion

Simulation_2_bs_exp_evo.R

• Simulates scenario ii where expression evolves under Brownian motion and abundance is 0.5 bar one tip, where it fluctuates (0 to 1)

Simulation_3_expandcomp_evo.R

• Simulates scenario iii where expression evoles under BM with varying covariances, and abundance is either 0.5 or is evolving under BM.

ERROR_RATE_1.R

• Script to calculate the type 1 error rate when running the same set of models as in scenario i but on a non-composite dataset (i.e. a single cell type). Type 1 error rate in this case is the percentage of cases where sigma² is not identified as 0 in a boostrapped BM model

ERROR_RATE_23.R

• Script to calcualte the type 1 error rate when running the same set of models as in scenario ii and iii but on a non-composite dataset (i.e a single cell type). Type 1 error rate in this case is the percentage of cases when the AICc value for an alternate model (OU or OU with a shift) is at least 2 less than that for a Brownian motion model.

Plot_Figures_123.R

• Script to calculate relative error rates in each of the scenarios and reproduce figures used in the manuscript.