gottacatchenall / metacommunitydynamics.jl Goto Github PK

This issue is used to trigger TagBot; feel free to unsubscribe.

If you haven't already, you should update your TagBot.yml to include issue comment triggers.
Please see this post on Discourse for instructions and more details.

If you'd like for me to do this for you, comment TagBot fix on this issue.
I'll open a PR within a few hours, please be patient!

Thanks for your work on this package! I'm trying to run any of the examples, but keep getting the following error for each one:

UndefVarError: fitnessmap not defined

I gather that this links with growth.jl and the LogisticGrowth() function. An MRE is just your introductory example:

## Load packages
using MetacommunityDynamics
using DynamicGrids
using Dispersal: OutwardsDispersal
using Distributions

## Define consumer equation
consumermodel = 
    Eating{Tuple{:C,:R}}(
        functionalresponse = LotkaVolterra(0.1), 
        dt = 0.1) +
    OutwardsDispersal{:C}() + 
    LinearMortality{:C}(0.3);

## Define producer equation
resourcemodel = 
    LogisticGrowth{:R}(λ = 2, K = 10., dt = 0.1) +
    LinearMortality{:R}(0.01) + 
    OutwardsDispersal{:R}();

## Put it together
model = resourcemodel + consumermodel

## Define metacommunity patch structure
gridsize = 10

## Initial conditions
initconsumer = rand(Biomass, Uniform(10, 30), gridsize, gridsize)
initresource = rand(Biomass, Uniform(10, 90), gridsize, gridsize)

## Integrate
arrayout = ArrayOutput((C = initconsumer, R = initresource ), tspan = 1:500)
sim!(arrayout, model);

• OS: Ubuntu 20.04
• Julia version: 1.7.1

v0.2

Features

• Environment types and generation via NL.jl integration
• Growth rates in response to environment

Enhancements

• Better default parameters for existing models
• Better printing via Term.jl

v0.3

Features

• Trait type that describes an arbitrary trait for particular species across space/time
• Growth rates proportional to traits in response to environment

v0.4

Features

• Selection on Traits in response to both environment and local community composition

v0.??

• speciation based on clustering traits

If you move the type of this field

https://github.com/gottacatchenall/EcoDynamics.jl/blob/327b87b4fbf47b1ced4263dcbb90009fa81c4c6a/src/problem.jl#L6

into the type declaration, you can dispatch on whether or not it has a spatial graph.