Earliest infections predict the age distribution of seasonal influenza A cases

Data and Code for Arevalo, et al., 2019 (Earliest infections predict the age distribution of seasonal influenza A cases).

Dependencies

• Miniconda with python 3.7

The required python and R packages can be installed by creating a conda environment with the included FluAImprinting.yml file as follows:

conda env create -f FluAImprinting.yml

Directory contents

• raw_data contains raw case data used to fit the model and other data sources used in the calculation of imprinting probabilities.
• data_processing contains scripts to reformat and refactor data.
• data contains data inputs used for modelling and imprinting probability calculation.
• models contains all models tested.
• fitting_scripts contains scripts used to fit models and process fit outputs.
• simulations contains scripts used to fit models to simulated data.
• vaccine_imprinting contains scripts used to fit models with imprinting conferred via vaccination.
• figures contains jupyter notebooks with code used to produce all figures in the manuscript.
• final_results_for_ms contains model fits used in the manuscript.

License

All files licensed under the Apache License, Version 2.0 (the "License"); you may not use these files except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.