calc_assortment: Calculate spatial segregation and assortment

In Waschina/Eutropia: Agent-based modelling of microbial communities in time and continuous µ-meter-scale space

Calculate spatial segregation and assortment

Description

This functions calculates cell-wise and mean cell type segregation and assortment values as suggested by Yanni et al. (2019) Current Biology.

Usage

calc_assortment(object, r = 5, iter = NULL, n_simulations = 10)

Arguments

object	S4-object of type growthSimulation.
r	Numeric. Maximum distance to to other cells to considered as neighbour. Refers to the surface-to-surface distance of cells. Unit: μm.
iter	Positive integer number of the simulation step/iteration at which the cell assortment should be calculated. If NULL, current distribution is displayed.
n_simulations	positive integer, specifying the number of permutations to be used to estimate the expected assortment if cell types are distributed randomly.

Details

Cell segregation and assortment is calculated as suggested by Yanni et al. (2019) Current Biology.

Value

A list with three elements: 'cells' is a data table with the cell-wise calculated segregation and assortment values. 'summary_observed' is a summary (mean and sd) of the observed segregation and assortment by cell types. 'summary_expected' is a summary of expected segregation and assortment if cell types are reassigned randomly to cells in the environment while maintaining the cell positions and community-wide cell type counts.

Waschina/Eutropia documentation built on Jan. 4, 2023, 12:42 p.m.