SymbulationEmp
Symbulation is an artificial life software tool for agent-based modeling of the evolution of biological symbiosis, which can occur along the spectrum between parasitism and mutualism.
Try out our browser-based GUI. See our documentation at https://symbulation.readthedocs.io.
Interested in starting a new project with Symbulation? We have a cookiecutter template here: https://github.com/anyaevostinar/SymbulationProjectTemplate.
Symbulation is built with the Empirical platform and the cookiecutter includes our recommended directory layout and example analysis files.
Usage
Install the latest Cookiecutter:
pip install -U cookiecutter
Generate an Symbulation project:
cookiecutter https://github.com/anyaevostinar/SymbulationProjectTemplate.git
Move into the new project directory and the SymbulationEmp directory and make:
cd SymbulationProject/SymbulationEmp
make
Make any changes that you wish to the file SymSettings.cfg and then run:
./symbulation_default
By default, your data will be output to the files HostVals_data__SEED10.data and SymVals_data__SEED10.data.
We recommend that you copy your symbulation executable to your Data folders:
cp symbulation_default ../Data/sample_treatment
cd ../Data/sample_treatment
You can then use the provided Python script to run several replicates:
python3 simple_repeat.py
You can also then use the provided Python script to transform your data into a format more easily used by R:
cd ../../Analysis/sample_treatment
python3 munge_data.py
And then open our provided R script SampleAnalysis.R in R, set your working directory to the Analysis directory and then run all lines to observe the effect of vertical transmission rate on the interaction value evolved.
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