How to use evofr

lfy · June 13, 2023, 3:58am

Dear nextstrain team, I’ve successfully installed evofr, but I don’t find ways to use the evofr to forecasts SARS-CoV-2.
I also can’t import my own data.

I would appreciate it if you could provide us with more details!

corneliusroemer · June 13, 2023, 11:42am

You can find some sample usage in this repo: GitHub - nextstrain/forecasts-ncov: SARS-CoV-2 variant growth rates and frequency forecasts

github.com

nextstrain/forecasts-ncov/blob/4acad345365b1164167b2edeee23fe067213953f/scripts/run-mlr-model.py#L9


      
          #!/usr/bin/env python
          # coding: utf-8
          
          
import argparse
          import pandas as pd
          import os
          import yaml
          import json
          import evofr as ef
          from datetime import date
          
          

          
def parse_with_default(cf, var, dflt):
              if var in cf:
                  return cf[var]
              else:
                  print(f"Using default value for {var}")
                  return dflt

github.com

nextstrain/forecasts-ncov/blob/4acad345365b1164167b2edeee23fe067213953f/scripts/run-renewal-model.py#L8


      
          #!/usr/bin/env python
          # coding: utf-8
          
          
import argparse
          import pandas as pd
          import os
          import yaml
          import evofr as ef
          
          

          
def parse_with_default(cf, var, dflt):
              if var in cf:
                  return cf[var]
              else:
                  print(f"Using default value for {var}")
                  return dflt

lfy · June 13, 2023, 12:45pm

Thank you very much for your reply.
I have found these two scripts, but I still don’t understand how to use them. For example, where should I input the path of my own metadata and what is the format requirement for the input file? Could you please provide a more detailed explanation?

lfy · June 13, 2023, 2:43pm

And if I conducted this Usage:
nextstrain build . --configfile config/config.yaml --config data_provenances=gisaid variant_classification=nextstrain_clades geo_resolutions=global
Do I need to change any parameters？

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How to use evofr

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