Quick start
Visit the Installation page to install phyddle.
To run a phyddle analysis enter the scripts
directory:
cd ~/projects/phyddle/scripts
Then create and run a pipeline under the settings you’ve specified in config.py
:
./run_phyddle.py -c config
This will run a phyddle analysis for a simple 3-region GeoSSE model with just 500 training examples. In practice, you’ll want to generate a larger training dataset with anywhere from 10k to 1M examples, depending on the model.
Provide phyddle with command-line options to customize how each pipeline step is executed. Visit Pipeline and Workspace to learn more about managing phyddle analyses. To add new examples to your training set, for example:
# [S]imulate new training examples, stored in
# workspace/simulate/my_project
./run_phyddle.py -s S -c config --start_idx 500 --end_idx 15000
# [F]ormat all raw_data examples as tensors,
# stored in workspace/format/my_project
./run_phyddle.py -s F -c config --start_idx 0 --end_idx 15000
# [T]rain network with tensor_data, but override batch size,
# stored in workspace/train/my_project
./run_phyddle.py -s T -c config --batch_size 256
# [E]stimate parameters for biological dataset, with results
# stored in workspace/estimate/my_project; and then [P]lot
# figures, storing them in workspace/plot/my_project
./run_phyddle.py -s EP -c config
Visit Configuration to learn more about currently supported phyddle settings. View supported command-line options with:
./run_phyddle.py --help