Alex M Chubaty

Alex M Chubaty

Ecologist and simulation modeller

FOR-CAST Research & Analytics

Professional Summary

Dr. Chubaty is an ecologist and simulation modeller who builds spatial models of forest landscapes and the species that live in them. He completed his PhD at Simon Fraser University modelling host selection in mountain pine beetle (MPB), followed by postdoctoral research at Université Laval and Natural Resources Canada developing forecasting models of MPB spread.

He runs FOR-CAST Research & Analytics in Calgary, Canada. His recent work includes LANDIS-II forest landscape simulation studies, landscape connectivity modelling, and analyses of insect outbreak dynamics, to inform land management and species-at-risk decisions. He writes open-source R packages for this work, including grainscape for connectivity analysis, landisutils for LANDIS-II simulations, and co-developed the SpaDES simulation platform. He advocates for open data and reproducible workflows.

Education

PhD in Biological Sciences

Simon Fraser University

BSc in Biological Sciences

University of Calgary

Interests

Forest landscape simulation Landscape connectivity Insect outbreak dynamics Wildlife habitat and species at risk Cumulative effects
Projects
Forest landscape simulation with LANDIS-II featured image

Forest landscape simulation with LANDIS-II

LANDIS-II simulation studies projecting forest succession and disturbance across large landscapes to inform forest management.

Habitat Connectivity featured image

Habitat Connectivity

Landscape connectivity modelling for wildlife habitat and protected area networks, including development of the `grainscape` R package.

Boreal forest ecosystem forecasts featured image

Boreal forest ecosystem forecasts

Integrated simulation models of forest vegetation dynamics, fire, insect disturbance, and wildlife populations, used to forecast boreal landscape change and inform management …

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 …

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

  • AGBtrends: Utilities for analyzing trends in above ground biomass. GitHub
  • bcwsft: BC Wildfire Service fuel typing algorithm (R port). GitHub
  • BiomeBGCR: Run Biome-BGC models from R. GitHub
  • CBMutils: Utilities for modelling carbon based on CBM-CFS3. GitHub
  • climateData: Utilities for working with North American climate data. GitHub
  • crew.ssh: ‘crew’ launcher plugin for SSH workers on a local network. GitHub
  • fireregimetools: Tools for summarizing fire regime statistics from simulations. GitHub
  • fireSenseUtils: Utilities for working with the ‘fireSense’ group of ‘SpaDES’ modules. GitHub
  • forestData: Tools for importing Canadian forestry data. GitHub
  • fpCompare: Reliable comparison of floating point numbers. CRAN; GitHub; Website
  • grainscape: Landscape connectivity, habitat, and protected area networks. CRAN; GitHub; Website
  • landisbc: British Columbia study-area tools for LANDIS-II workflows. GitHub
  • landisutils: Utilities for preparing, running, and post-processing LANDIS-II simulations. GitHub; Website
  • LandR: Landscape Ecosystem Modelling in R. GitHub; Website
  • LandWebUtils: Additional utilities for LandWeb analyses. GitHub; Website
  • libcbmr: Interface to the Carbon Budget Model library based on CBM-CFS3. GitHub
  • map: Defines a meta class of geographical objects, the ‘map’ class, and associated tools. GitHub; Website
  • mpbutils: Utilities for mountain pine beetle simulation modelling. GitHub
  • NetLogoR: Build and run spatially explicit agent-based models. CRAN; GitHub; Website
  • nrvtools: Tools for summarizing outputs from natural range of variability simulations. GitHub
  • pemisc: Miscellaneous utilities developed by the Predictive Ecology Lab Group. GitHub; Website
  • peutils: Utilities developed by the Predictive Ecology Group. GitHub; Website
  • sbwutils: Utilities for modelling spruce budworm eruptions across Canada. GitHub
  • scfmutils: Tools and utilities for working with the SCFM wildfire simulation model. GitHub; Website
  • SpaDES.targets: Orchestrate SpaDES simulations with ’targets’. GitHub
  • spatialutils: Utilities for working with spatial data. GitHub
  • workflowtools: Project workflow management tools and utilities. GitHub
  • ytdata: Fetch Yukon open geospatial data. GitHub

SpaDES simulation platform (co-developer)

  • quickPlot: A system of plotting optimized for speed and modularity. CRAN; GitHub; Website
  • reproducible: Enhance reproducibility of R code. CRAN; GitHub; Website
  • SpaDES: Metapackage for the SpaDES family. GitHub; Website
  • SpaDES.addins: Tools and RStudio addins for ‘SpaDES’ module development. GitHub
  • SpaDES.core: Core utilities for developing and running spatially explicit discrete event models. CRAN; GitHub; Website
  • SpaDES.docs: Helper utilities for creating SpaDES module documentation and manuals. GitHub; Website
  • SpaDES.experiment: Simulation experiments within the SpaDES ecosystem. GitHub; Website
  • SpaDES.tools: Additional tools for developing spatially explicit discrete event simulation (SpaDES) models. CRAN; GitHub; Website

Contributor

  • BioSIM: Client for the BioSIM web API. GitHub
  • J4R: Create ‘Java’ objects and execute ‘Java’ methods. GitHub
  • LandR.CS: Climate-sensitive growth and mortality in LandR. GitHub
  • lazyR: Create lazy load databases for R objects. GitHub
  • miniCRAN: Create a mini version of CRAN containing only selected packages. CRAN; GitHub; Website
  • PSPclean: Sources and standardizes permanent sample plot data. GitHub
  • Require: Installing and loading R packages for reproducible workflows. CRAN; GitHub; Website
  • SpaDES.project: Project templates using ‘SpaDES’. GitHub; Website
  • tiler: Create geographic and non-geographic map tiles. CRAN; GitHub; Website

LANDIS-II contributions

  • LANDIS-II Docker and Apptainer images: containers with LANDIS-II and its extensions, for workstations and computing clusters. GitHub
  • LANDIS-II extensions: build fixes for 13 extensions (library references, including the Universal Cohort Library v2 update), a bug fix in ForCS Succession, and documentation updates for Base Fire and Biomass Succession. GitHub
  • LANDIS-II Forest Product Sector extension: carbon transfers and emissions from harvested wood products. 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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+1.403.708.5790