Selection Matrix

What is a selection matrix?

A selection matrix is a map specifying how the parental communities are selected according to their function ranks, and how the selected communities are pooled or distributed to seed the offspring communities. It is a square matrix of size n_wells. The columns are ranked parental communities and the rows are offspring communities. Each element in the selection matrix specifies the dilution factor used for the batch culture.

The selection matrices allow us to standardize most strategies of artificial community selection, for example, propagule and migrant pool approaches, into a regular form.

How does selection matrix work in ecoprospector?

A selection matrix is written in the form of a Python function to accommodate a varied number of communities in different independent experiments. These functions take a vector of values (the default output of Community Function functions) as input. The selection matrix function will read the length of the input vector, and construct a selection matrix of that length. The selection matrix is then used to guide the passaging of the metacommunity.

A selection matrix must be defined during the simulation setup, i.e. stored in the C_selection_matrices.py. During simulation, any particular selection matrix will be called according to Selection Protocol.

A library of selection matrices

We saved all the predefined selection matrices in C_selection_matrices.py. These selection matrices were adapted from the selection protocols in the prior empirical and theoretical studies.