About the titer model
Running the titer model
This model was originally published in Neher et al (PNAS, 2016) and implemented as part of the Nextstrain augur package. The relevant portions of the repository have been reproduced here under
implementation-nextstrain-augur. Documentation, including install instructions, for the full augur pipeline can be found here. Note that for future reuse, I would actually recommend running the model via the newly modularized implementation here.
1 - Prepare input files
dengue.prepare.py handles subsampling and other basic dataset config. You can edit the function
make_config here with any desired changes.
cd dengue-antigenic-dynamics/titer_model/implementation-nextstrain-augur/builds/dengue/ python dengue.prepare.py #--options
NB: For this dataset, step 1 has been run for you; see
2 - Run the titer pipeline (and estimate clade frequencies)
dengue.process.py handles the actual analysis; parameter settings, etc. can be changed in the
make_config function here.
python dengue.process.py -j path_to_prepared_json
NB: For this dataset, step 2 has been run for you; see
3 - Check out your results
Results are output in JSON format, found in
./processed/. You can parse and examine results using the notebook found here.