Execution

After you have installed and configured RAPIDS, use the following command to execute it.

./rapids -j1

Info

The script ./rapids is a wrapper around Snakemake so you can pass any parameters that Snakemake accepts (e.g. -j1).

Updating RAPIDS output after modifying config.yaml

Any changes to the config.yaml file will be applied automatically and only the relevant files will be updated. This means that after modifying the features list for PHONE_MESSAGE for example, RAPIDS will update the output file with the correct features.

Multi-core

You can run RAPIDS over multiple cores by modifying the -j argument (e.g. use -j8 to use 8 cores). However, take into account that this means multiple sensor datasets for different participants will be load in memory at the same time. If RAPIDS crashes because it ran out of memory reduce the number of cores and try again.

As reference, we have run RAPIDS over 12 cores and 32 Gb of RAM without problems for a study with 200 participants with 14 days of low-frequency smartphone data (no accelerometer, gyroscope, or magnetometer).

Forcing a complete rerun

If you want to update your data from your database or rerun the whole pipeline from scratch run one or both of the following commands depending on the devices you are using:

./rapids -j1 -R download_phone_data
./rapids -j1 -R download_fitbit_data

Deleting RAPIDS output

If you want to delete all the output files RAPIDS produces you can execute the following command (the content of these folders will be deleted: data/raw, data/interim, data/processed, reports/figures, and reports/compliance)

./rapids -j1 -R clean

Ready to extract behavioral features

If you are ready to extract features head over to the Behavioral Features Introduction