The titer model seeks to assign discrete units of antigenic change to specific mutations across the dengue phylogeny. Full model details can be found in Neher et al. and our preprint.
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.
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 ./implementation-nextstrain-augur/dengue/prepared/titered.json
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 ./titered_output/
Results are output in JSON format, found in ./processed/. You can parse and examine results using the notebook found here.