We want to focus our simulations on just the pathogen types we actually analyze, so we don’t need to include all types of recombination.
The primary purpose of simulations is to understand the optimal embedding parameters for a given type of pathogen without overfitting those parameters to real data.
A secondary purpose of simulations is to understand how embeddings represent known populations through time.
We want to use only H3N2-like and moderate-recombination coronavirus-like simulations to tune parameters for H3N2 and SARS-CoV-2.
We want to focus our simulations on just the pathogen types we actually analyze, so we don’t need to include all types of recombination.
The primary purpose of simulations is to understand the optimal embedding parameters for a given type of pathogen without overfitting those parameters to real data.
A secondary purpose of simulations is to understand how embeddings represent known populations through time.
We want to use only H3N2-like and moderate-recombination coronavirus-like simulations to tune parameters for H3N2 and SARS-CoV-2.