Spatial Package Use Clarification

[bur...@miamioh.edu]

Hello,

I'm currently attempting to model quorum sensing in dictyostelium populations as described here: https://www.ncbi.nlm.nih.gov/pubmed/26172740. Specifically, I'm modeling the case near the end of the paper when they simulate an entire population in 2d space. The model includes two species: one for extracellular cAMP and one for the dictyostelium cells. The simulation space is then just one domain in which the cAMP and the cells coexist.

I'm having a hard time however deciding how exactly to specify the geometry definition (as described in the spatial package). Of the 5 available, I'm fairly certain that I should either be using AnalyticGeometry, SampledFieldGeometry or ParametricGeometry. In what cases would one use AnalyticGeometry or Parametric Geometry? I'm feeling as if SampledFieldGeometry would be the way to go but it seems that it will hardcode the spatial resolution which is undesirable (in an ideal case, the simulation spatial resolutions of the cAMP species and of the dictyostellium species need not be the same).

I understand that the spatial package is still under development but I would rather use that than create my own nonportable extension.

[Frank Bergmann]

Hello,

I'm not sure I am absolutely certain what you are after. Let us take
for example the spatial simulations of Figure 7 in the referenced
publication. The easiest geometry you could use for that would be to
use an AnalyticGeometry, with a math of 1. That would basically give
you the whole defined coordinate system as the domain.

In our work we use mainly analytic geometries, where we layer domains
over each other. Or we use the sampledFieldGeometry if we import the
geometry from microscopy data.

best
Frank

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