Specifying population structure
This page describes how users specify the names, sizes, and connectivities of the different subpopulations comprising the total population to be modeled
The subpop_setup section of the configuration file is where users can input the information required to define a population structure on which to simulate the model. The options allow the user to determine the population size of each subpopulation that makes up the overall population, and to specify the amount of mixing that occurs between each pair of subpopulations.
An example configuration file with the global header and the spatial_setup section is below:
Items and options
Config Item
Required?
Type/Format
Description
geodata file and selected option
geodata is a .csv with column headers, with at least two columns: subpop and population.
selected if provided, is the subset of locations in geodata file (as determined by subpop column) to be modeled. Requesting subpopulation(s) that are not present will lead to an error.
Example geodata file format
The mobility file is a .csv file (it has to contain .csv as extension) with long form comma separated values. Columns have to be named ori, dest, amount, with amount being the average number individuals moving from the origin subpopulation ori to destination subpopulation dest on any given day. Details on the mathematics of this model of contact are explained in the . Unassigned relations are assumed to be zero. The location entries in the ori and dest columns should correspond to an entry in the subpop column in geodata.csv. When using selected
Example mobility file format
It is also possible, but not recommended to specify the mobility file as a .txt with space-separated values in the shape of a matrix. This matrix is symmetric and of size K x K, with K being the number of rows in geodata. The above example corresponds to
To simulate a simple population structure with two subpopulations, a large province with 10,000 individuals and a small province with only 1,000 individuals, where every day 100 residents of the large province travel to the small province and interact with residents there, and 50 residents of the small province visit the large province
geodata.csv contains the population structure (with columns subpop and population)
mobility.csv contains