Alex M Chubaty

Alex M Chubaty

Ecologist and simulation modeller

FOR-CAST Research & Analytics

Professional Summary

Dr. Chubaty is an ecologist, simulation modeller, and co-developer of the open source SpaDES simulation platform. He completed his PhD at Simon Fraser University modelling host selection in mountain pine beetle (MPB), and postdoctoral research at Université Laval and Natural Resources Canada developing forecasting models of MPB spread.

He currently operates FOR-CAST Research & Analytics in Calgary, Canada, which supports the development and integration of models simulating forest vegetation dynamics, wildfire, insect disturbance, and wildlife populations to inform decision making for land management and species at risk. He is an advocate for open source, open data, and reproducible workflows.

Education

PhD in Biological Sciences

Simon Fraser University

BSc in Biological Sciences

University of Calgary

Interests

Insect outbreaks Forest ecology Cumulative effects Simulation modelling
Projects
Habitat Connectivity featured image

Habitat Connectivity

We have reimplemented and updated the `grainscape` R package for landscape connectivity, habitat, and protected area network analyses.

Boreal forest ecosystem forecasts featured image

Boreal forest ecosystem forecasts

We are integrating various simulation models dealing with forest vegetation dynamics, fire, insect disturbance, and wildlife populations, to inform decision making in these …

Eruptive Insect Dynamics featured image

Eruptive Insect Dynamics

Major forest insect pests in Canada (forest tent caterpillar, spruce budworm, and mountain pine beetle) share a common feature: their populations exhibit *eruptive* (nonlinear, …

LandWeb: historic range of variation in western boreal forests featured image

LandWeb: historic range of variation in western boreal forests

LandWeb is the first large scale, data-driven approach to simulating historic natural ranges of variation (H/NRV). This model integrates two well-used models for forest stand …

Simulating mountain pine beetle eastward spread featured image

Simulating mountain pine beetle eastward spread

The continued eastward spread of mountain pine beetle (*Dendroctonus ponderosae* Hopk.; MPB) now threatens the boreal forests of eastern Alberta, Saskatchewan, and beyond. …

Recent Publications
Recent & Upcoming Talks

Cumulative effects research in SpaDES

Natural resource management decisions benefit from cumulative effects research that efficiently integrates scientific knowledge across multiple disciplines in a timely manner. Unfortunately, researchers frequently encounter barriers to efficient integration, especially when it comes to data, models, and analyses, due to the inaccessibility and non-interoperability of these components, which contributes to disciplinary ‘siloing’ and can delay scientific outputs. Using modern tools to facilitate a continuous and adaptive workflow, I present an overview and results from two recent large scale simulation studies developed using the SpaDES package for R. I reflect on the successes and the challenges of these projects, and highlight key insights from the processes implemented for them.

Software

Author

  • fpCompare: Reliable comparison of floating point numbers. CRAN; GitHub; Website
  • grainscape: Efficient modelling of landscape connectivity, habitat, and protected area networks. CRAN; GitHub; Website
  • LandR: Landscape Ecosystem Modelling in R. GitHub; Website
  • LandWebUtils: Additional utilities for LandWeb analyses. GitHub; Website
  • map: Defines a meta class of geographical objects, the ‘map’ class, and associated tools. GitHub; Website
  • NetLogoR: A Port of ‘NetLogo’ Functions and Language to R. CRAN; GitHub; Website
  • pemisc: Miscellaneous utilities developed by the Predictive Ecology Lab Group. GitHub; Website
  • quickPlot: Develop and run spatially explicit discrete event simulation models. CRAN; GitHub; Website
  • reproducible: Develop and run spatially explicit discrete event simulation models. CRAN; GitHub; Website
  • SpaDES: Develop and run spatially explicit discrete event simulation models. CRAN; GitHub; Website
  • SpaDES.addins: Tools and RStudio addins for ‘SpaDES’ and ‘SpaDES’ module development. CRAN; GitHub; Website
  • SpaDES.core: Core functionality for Spatial Discrete Event Simulation (SpaDES). CRAN; GitHub; Website
  • SpaDES.experiment: Simulation experiments within the SpaDES ecosystem. GitHub; Website
  • SpaDES.shiny: Utilities for building shiny-based apps for SpaDES simulations. GitHub; Website
  • SpaDES.tools: Additional modelling tools for Spatial Discrete Event Simulation (SpaDES) module development. CRAN; GitHub; Website

Contributor

  • miniCRAN: Create a mini version of CRAN containing only selected packages. CRAN; GitHub
Recent Posts

Using the latest GDAL with R packages on macOS - redux

As an update to an earlier post, here’s how to use the latest versions of GDAL/PROJ with R spatial packages.

Install GDAL

brew install pkg-config
brew install gdal

(Re)install R spatial packages

Next, we need to install a few packages from source in order to use the new GDAL libraries:

Using the latest GDAL with R packages on macOS

UPDATE: see more recent version of this post here.

I wanted to play around with the new sf package, which requires the latest GDAL (>= 2.0.0), GEOS (>= 3.3.0), and PROJ.4 (>= 4.8.0). However, the version of GDAL installed via brew is 1.11.4, so I needed to update to the latest version and reinstall a few R packages in order to get sf to work on macOS.

meow: the most anticipated R package of 2015

In preparing a presentation on developing R packages using RStudio for the Victoria R Users Meetup Group this month, organizer Kiri Whan and I put together a very simple demo R package.

Installing rgdal on OSX

This is actually really easy to do, but most of the google hits I came across were old (from 2010) or horribly complex (building gdal and proj4 from source then building rgdal itself).

Contact

Contact

I'm always open to discussing new projects, opportunities, or just having a chat.

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Call me

+1.403.708.5790