README.md

Configuration Files

These files contain variables for repository path, output data path, data paths, etc. The variables must be changed to be computer/project specific.

Specifically, the following change is required within the config.R file:

PROJECT_PATH (location of the infection-timing repository) and OUTPUT_PATH (location where output files should be stored) variables

Within the file_paths.R file, the following changes are required:

TRAINING_INFANT_DATA_PATH (file path for the training data set) and TRAINING_INFANT_METADATA_PATH (file path for the training data set meta data)
TESTING_INFANT_DATA_PATH (file path for the testing data set) and TESTING_INFANT_DATA_TRUE_TIME_PATH (file path for the true infection times for the training data set)