Examples

This module contains examples of how to assemble and modify models in MIRA.

Curated Example Models

sir.py - Simple examples of SIR epi models
chime.py - Simple example of a SVIIvR epi model
mech_bayes.py A curated model describing the Mech Bayes model (an SEIRD epi model).
nabi2021.py A curated model describing the Nabi et al. 2021 model (an ‘SEIQAIRDL’ epi model). See https://doi.org/10.1016/j.chaos.2021.110689 for more information.
jin2022.py A curated model describing the Jin et al. 2022 model, describing a vaccine-stratified epi model.

Decapode Examples (`mira.examples.decapodes.decapodes_examples`)

get_ice_dynamics_example()[source]

Return the ice dynamics decapode example

Return type:: Decapode
Returns:: The ice dynamics example as a Decapode object

get_ice_decapode_json()[source]

Return the ice dynamics decapode example as json

Returns:: The ice dynamics example as a json object
Return type:: JSON

get_budyko_sellers_example()[source]

Returns the budyko sellers decapode example

Return type:: Decapode
Returns:: The budyko-sellers example as a Decapode object

get_budyko_seller_decapode_json()[source]

Return the budyko sellers decapode example as json

Returns:: The budyko-sellers example as a json object
Return type:: JSON

get_oscillator_decapode()[source]

Return the oscillator decapode example

Example from

Return type:: Decapode
Returns:: The oscillator example as a Decapode object

get_oscillator_decapode_json()[source]

Return the oscillator decapode example as json

Returns:: The oscillator example as a json object
Return type:: JSON

get_friction_decapode()[source]

Return the friction decaexpr example

Return type:: Decapode
Returns:: The friction example as a Decapode object

get_friction_decapode_json()[source]

Return the friction decaexpr example as json

Returns:: The friction example as a json object
Return type:: JSON

get_oscillator_decaexpr()[source]

Return the oscillator decaexpr example

Return type:: Decapode
Returns:: The oscillator example as a Decapode object

get_friction_decaexpr()[source]

Return the friction decaexpr example

Return type:: Decapode
Returns:: The friction example as a Decapode object

Decapodes vs DecaExpr Composite models

This directory, mira/examples/decapodes/decapodes_vs_decaexpr_composite , contains the components of the composite model example at https://algebraicjulia.github.io/SyntacticModels.jl/dev/generated/composite_models_examples/

DecaExpr JSON files

The DecaExpr JSON files are copied from the model fields of the full composite JSON output found in the link above.

Decapodes JSON files

The decapodes JSON files are generated from the DecaExpr julia models by running the following code (in julia). To run this code, julia has to be installed. Then the dependencies need to be installed as well. julia is pretty explicit about what needs to be installed, so if you have julia installed and try to run this code, it will tell you what needs to be installed if any dependencies are missing and how to do it. Typically, it involves running import Pkg; Pkg.add("PackageName") in the julia REPL.

# The code here mostly follows the code in
# https://algebraicjulia.github.io/SyntacticModels.jl/dev/generated/composite_models_examples/

using SyntacticModels

using SyntacticModels.AMR
using SyntacticModels.ASKEMDecapodes
using SyntacticModels.ASKEMUWDs
using SyntacticModels.Composites

using MLStyle
import SyntacticModels.ASKEMDecapodes.Decapodes as Decapodes
using Catlab
using Catlab.RelationalPrograms
using Catlab.WiringDiagrams
using Test
using JSON3

# Import Decapodes to access SummationDecapode; Avoid name collision
import Decapodes as DecapodesModule

# Specifying the Composition Pattern
x = Typed(:X, :Form0)
v = Typed(:V, :Form0)
Q = Typed(:Q, :Form0)
variables = [x,v,Q]

c = [x, Q]
s = [Statement(:oscillator, [x,v]),
     Statement(:heating, [v,Q])]
u = ASKEMUWDs.UWDExpr(c, s)

# Specifying the Component Systems
h = AMR.Header(
    "harmonic_oscillator",
    "modelreps.io/DecaExpr",
    "A Simple Harmonic Oscillator as a Diagrammatic Equation",
    "DecaExpr",
    "v1.0"
)

dexpr = Decapodes.parse_decapode(quote
    X::Form0{Point}
    V::Form0{Point}

    k::Constant{Point}

    ∂ₜ(X) == V
    ∂ₜ(V) == -1*k*(X)
end
)

# Model 1
d1 = ASKEMDecaExpr(h, dexpr)

# Model 2
d2 = ASKEMDecaExpr(
  AMR.Header("fricative_heating",
   "modelreps.io/SummationDecapode",
   "Velocity makes it get hot, but you dissipate heat away from Q₀",
   "SummationDecapode", "v1.0"),
    Decapodes.parse_decapode(quote
      V::Form0{Point}
      Q::Form0{Point}
      κ::Constant{Point}
      λ::Constant{Point}
      Q₀::Parameter{Point}

      ∂ₜ(Q) == κ*V + λ*(Q - Q₀)
    end)
)

# Create a header for the decpode version of model 1
decpode1_header = AMR.Header(
    "harmonic_oscillator",
    "modelreps.io/SummationDecapode",
    "A Simple Harmonic Oscillator",
    "SummationDecapode",
    "v1.0"
)

# Create the decpode version of model 1
# The transformation from DecaExpr to Decapode is done by the SummationDecapode function on the model
d1_decapode = ASKEMDecapode(decpode1_header, DecapodesModule.SummationDecapode(d1.model))

# Repeat for model 2
decpode2_header = AMR.Header(
    "fricative_heating",
    "modelreps.io/SummationDecapode",
    "Velocity makes it get hot, but you dissipate heat away from Q₀",
    "SummationDecapode",
    "v1.0"
)
d2_decapode = ASKEMDecapode(decpode2_header, DecapodesModule.SummationDecapode(d2.model))

# Write the decapode JSON files
write_json_acset(d1_decapode.model, "d1_oscillator_decapode.json")
write_json_acset(d2_decapode.model, "d2_friction_decapode.json")

Load Decapode JSON files into MIRA Decapode class

The Decapode JSON files can be loaded into the MIRA Decapode class by running the following code:

from mira.examples.decapodes.decapodes_examples import get_oscillator_decapode, get_friction_decapode

oscillator_decapode = get_oscillator_decapode()
friction_decapode = get_friction_decapode()

Load DecaExpr JSON files into MIRA DecaExpr class

The DecaExpr JSON files can be loaded into the MIRA Decapode class by running the following code:

from mira.examples.decapodes.decapodes_examples import get_oscillator_decaexpr, get_friction_decaexpr

oscillator_decaexpr = get_oscillator_decaexpr()
friction_decaexpr = get_friction_decaexpr()