New users who want to run evofr on their own pathogen data need some guidance about how to use the new evofr prepare-data and evofr run-model command line tools. The simplest solution could be a quickstart guide in the repository's README that shows what the minimal inputs are for preparing data, running the model, and inspecting the model outputs. I'd recommend developing the guide based on open SC2 data, since evofr has been applied to these data most frequently.
Encouraging further use of this interface could also help us move away from custom implementations of these tools in other repositories.
New users who want to run evofr on their own pathogen data need some guidance about how to use the new
evofr prepare-dataandevofr run-modelcommand line tools. The simplest solution could be a quickstart guide in the repository's README that shows what the minimal inputs are for preparing data, running the model, and inspecting the model outputs. I'd recommend developing the guide based on open SC2 data, since evofr has been applied to these data most frequently.Encouraging further use of this interface could also help us move away from custom implementations of these tools in other repositories.