Closed mastrof closed 5 months ago
Main issue I have here is that defining the transition matrix manually would be very cumbersome. There needs to be some convenient interface
EDIT: not a big deal, the cumbersome part can be easily hidden from the user
Other issue, may be more significant: using Motility{N}
introduces the extra parameter N
to all subtypes of AbstractMicrobe
; this means that on model initialization one must specify e.g. StandardABM(Microbe{2,N},...)
which would restrict the model to only microbes with N-state motile patterns, or require unions to allow for different motility patterns within the same simulation, which is quite inconvenient
The current implementation of motility types is cumbersome, not easily extendable and even incomplete.
Ideally, it would be nice to implement a single
Motility{N}
type withN
being the number of motile states, with the switches between such states defined by a transition matrix.The states would need to contain all the information required for the microbe stepping and the transition to other states (e.g. speed of motion, reorientation distributions, average lifetime of the state...).
Ideally, this could be something as simple as
but I'm not yet sure if having a unique
MotileState
type to represent all sorts of behaviors (runs, tumbles, stops....) makes sense