In PredictiveEcology/SpaDES.Workshops: Training workshops for ecological modeling with SpaDES

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SpaDES

Spatial Discrete Event Simulator

• Discrete event simulators have a long history in computer science
• SpaDES is oriented around the construction of spatially explicit models and the use of spatial data.
• events describe changes in the state of a complex system at some time
• time is not modeled in a continuous fashion (simple loops would do this); we can 'skip ahead' to the next event, speeding up model evaluation
• events are scheduled (added to a queue) dynamically, and executed at their scheduled time

Other DESs

• In Ecology, there are other generic DESs:

  • SELES (very generic)
  • HexSim
  • NetLogoR (individual based models)

• More specific DESs

  • LANDIS-II (forest dynamics)

Events

• Spring thaw
  
  
• Brainstorm events...

Modules

• Modules are a convenient way to group events that fit naturally together:

  • e.g., fire ignition module
  • e.g., carbon accumulation module
  • e.g., data preparation module

• What is contained in one module is highly idiosyncratic .

Modules → Modularity

SpaDES is implemented in a way that facilitates modularity of code:

• different (ecological) processes can be grouped into logical units (modules)
• a(n) (ecological) model consists of a collection of modules
• each module is responsible for scheduling its own events
• modules interact indirectly via shared data objects (e.g., a map); module 'A' doesn't need to know what module 'B' is doing

Thus, modules can be added, removed, or swapped out without needing to recode the rest of the model.

Module types

• There are many types of modules that may be useful:

  • Agents
  • Events
  • Data preparation
  • Summaries of data
  • see list from SpaDES wiki

Once we see that a module is just a convenient way to group together events, anything can be a module. Can be a single line of code or as many as you want.

Agent-based modules

• caribou
• wolfAlps
• Mountain Pine Beetle

Raster module

• Vegetation change
• Spatial clustering (e.g., to create polygons)
• Aging
• Class change (e.g., land cover class)
• Biomass change
• etc.

Data preparation module

• cropReprojectLcc

Why use a SpaDES module

... instead of just an R script or function?

• allows things to be scheduled

• allows modularity

  • a module can be reused by someone else with little change

• can be published on the web

• can estimate unknown parameters
• and much more...

Anatomy of a module

A module is an R script with 3 parts:

1. Metadata - a list of 15 things

   • Name, Author, Description, other for human reader
   • parameters, input objects, output objects for R to "understand"

2. doEvent - 2 types of things here

   • schedule events
   • run functions

3. Anything else

   • e.g., initial data preparation steps

Running SpaDES

Essentially 2 steps

1. Create a simList using simInit()
2. Run spades()

All the necessary information is contained within the simList

What might be needed for a DES to run...

What is in the simList

- start and stop times
- data
- paths
- which modules to use
- parameters
- a schedule of events
- outputs

(Will be covered in detail later)

Data

• We are working with R, so we can use any data structure or file format that R can understand

• SpaDES has some helpers for loading data, but in general, the module should be explicit

  • e.g., downloadData("caribouMovementLcc", path = tempdir())

• A module takes input data, changes them, and provides outputs

• like a function, but with the addition of "time"

• Some challenges ...

Data challenges

Numerous challenges exist with data

• messy
• ownership
• large
• permissions
• errors
• other

SpaDES doesn't necessarily solve these issues, but in some cases it helps.

Where to get help

• package help docs (e.g., overview of SpaDES package):

?SpaDES

• package vignettes (link)
• SpaDES wiki (link)
• SpaDES user group (link)
• bug reports (link)

PredictiveEcology/SpaDES.Workshops documentation built on Jan. 30, 2021, 6:52 p.m.