Welcome

Welcome to the online Habitat Ecosystem Assessment Tool (HEAT). If you are new to the HEAT framework, consider starting with the Conceptual Overview below.

To begin a new assessment, please work through the steps listed on the left in order. Each step includes a Quickstart guide at the top of the page, but please refer to the HEAT Manual for more information on best practices, underlying assumptions, and data sources used.
Tip

HEAT is currently under maintenance, please do not use the tool at this time. If you need to use the tool urgently please reach out to the GLLFAS Habitat Assessment inbox for guidance.

Conceptual Overview

HEAT is a tool that aims to predict how a set of physical modifications to a study area will affect the overall habitat suitability for all fish species in the region. Using this framework, users can assess the potential impacts of planned nearshore developments, make more informed decisions on how best to restore degraded aquatic habitats, and address other questions about how specific changes to aquatic habitats affect the fish assemblages that occupy them.

A complete HEAT analysis consists of five key steps:

1. Define fish list

HEAT includes default fish species lists for large lakes and all tertiary watersheds in Canada. Users define the species list for their assessment area by pinpointing the area on HEAT’s interactive map or by selecting watersheds by name.

2. Grouping by Guild

Since most HEAT analyses consider a very large number of species, it is often impractical to visualize the effect of a given habitat modification on each species in isolation. Instead, we group species into guilds based on similar habitat or resource requirements to visualize the average impact on each guild or guild grouping.

3. Calculating Habitat Suitability Matrix (HSM)

The Habitat Suitability Matrix (HSM) assigns a habitat suitability score to various habitat features for each species and life stage. In this step, users must decide which habitat features they want to consider in their analysis and generate an appropriate HSM.

4. Defining Scenarios

HEAT uses a tabular format to represent both the habitat features present in the assessment area and how these features change between pre and post scenarios. In this step, users must provide this information by filling out and uploading a template spreadsheet.

5. Run Weighted Suitable Area (WSA) Analysis

The final step combines the species information in the HSM with the habitat information defined in the scenarios spreadsheet to calculate the net change in suitable habitat for each species and guild. Once the analysis has run, you can view a summary table and overview plot in the web app, or download the full report for further analysis.

Updates

Lifecycle: stable

Note: Feedback or suggestions regarding this app can be sent to the GLLFAS Habitat Assessment inbox.

2025-04-09

  • Fix major bug with guild assignments in Habitat Suitability Matrix

2025-03-20

  • Add Longear Sunfish to Bay of Quinte AOC fish list
  • Update guild assignment of Longnose Sucker and Mottled Sculpin

2024-08-28

  • Add water temperature module to model
  • Add age-specific species vegetation preference information
  • Consolidate reporting of missing and excluded fish species

2024-08-16

  • Better standardize warning messages across modules
  • Better validation of guild grouping variables and habitat variables

2024-07-10

  • Add selected watersheds and excluded species to report
  • Add option to use AOC-specific fish lists and notification when relevant watersheds are selected
  • Add checks, warning, and reporting of non-contiguous watershed selection

2024-06-10

  • Minor clean up of UI elements
  • Update dependencies and deprecated function calls
  • Minor clean up and bug fixes to output report

2024-03-18

  • Add optimizations to WSA calculation
  • Minor bug fixes to substrate names
  • Internal restructuring

2024-02-13

  • Add static quickstart docs
  • Lock out steps until pre-requisites are met
  • Minor bug fixes and additions to output report
  • Minor optimizations to map rendering and selection

2023-06-29

  • Replace COMM with OFFM in area description (AreaType) of SampleData.xlsx
  • Replaced HEAT Logo with SVG located in www folder
  • Update to Development Manual, issue addressing port 81 from DFO network
  • fixes, code clean up

2023-06-16

  • Added in detailed glossary, corrected the order of substrate (cobble and rubble order), and changed CI to QAF to match current documentation.
  • Added css to highlight save on mouse over
  • Change docker build command script to reduce size of image by 1.5G

2023-05-29

  • Fixes, write excel report function, over writing template headers and a minor typo of HSM

2023-05-26

  • Added download excel report module
  • Added blank downloadable template excel file

2023-05-15

  • Fix, incremented minimum version of ggplot2 package to 3.4.0

2023-04-28

  • Side menu font size increased
  • Removed WSA calculation button, calculation triggered on WSA tab page load.
  • Update fct_plot_wsa_output.R - Modified size of labels and other elements in plot to make it easier to read.
  • Update fct_calculate_WSA.R - Replace YOY label for life stage with Nursery label.
  • Update mod_03_guild_grouping.R - Changed header to indicate recommendation to only select two guild grouping variables max.
  • Update fct_calc_HSM.R - Updated function so that HSIs are calculated using a geometric mean approach.

2023-04-14

  • Added shinycustomloader package for waiter animation used in WSA analysis module
  • Fixes and code clean up
    • Set LazyDataCompression field to improve performance, some data sets not saved with type of compression flag set
    • Incremented minimum version of R, some data sets saved under version 3.5.0
    • Added some of the developers contact information to the package

2023-03-31

  • Added in ability to plot WSA output
  • Added WSA Summary output
  • Fixes, code clean up and commenting
  • Updated minimum version of dplyr and shiny

2023-03-20

  • Rewrote Scenario modules reversing changes made on 2022-06-10, It streamlined the code, eliminated sources of errors and returned functionality similar to reference code HEATv1 package.
    • Functionality lost manual data entry, and multiple post scenarios entry.
    • Gained, The ability to upload scenarios from spreadsheet template

2023-03-08

  • Added Sample file Download Feature

2023-02-27

  • Changed docker base to rocker/r-ver:4.2.2
  • Update “spelling” package to minimum version 2.2

2022-12-23

  • Rewrote the WSA module including:
    • Modifications to make the old function work with updated package
    • Added example date data/sample_scenarios.rda
  • Fixes and package update
    • Added janitor package used in WSA calculate function to dev.R script, Docker, package NAMESPACE and DESCRIPTION files
    • Fix Docker file, package “spelling” had “NA” in version parameter field causing docker build to crash

2022-12-16

  • Rewrote the HSM function
  • Rewrote the guild grouping function including:
    • Corrections to ensure species were assigned to the correct guild
  • Updated base tables including:
    • Addition of vegetation guild data for several guilds that have species requirement data (Shortnose Cisco, Chum Salmon, Atlantic Salmon, Arctic Char, and Common Carp)
    • Minor spelling mistakes corrected

2022-06-10

  • Rewrote the Scenario module including:
    • Scenarios are now edited in browser instead of downloading/uploading a spreadsheet.
    • Can load example data with one button.
    • Can copy pre project information to post project and edit them.
    • Ability to create 1-3 post project scenarios.
    • Added a Save button to restore the state of the application.

2022-06-05

  • Added an additional “Missing fish” box to the Habitat Suitability module. This box will show all fish that have been dropped due to missing guild grouping or habitat suitability information. The output of this box will update with the life stage selected.
  • The HSM table now shows percentages and rounds to two decimal places to improve readability.
  • Improved existing and added additional validation and error handling.

2022-06-03

  • Rewrote the Grouping and Weights module including:
    • Added a “Missing fish” box to show which fish are excluded from the analysis because they are missing guild grouping information.
    • A number of options for grouping species (such as by Family, Genus, Spawning Temperature, and Status) have been removed to make the tool simpler.
    • The ability to change the weights of life stages or guilds has also been removed. In most scenarios, these should not have been modified anyway.
    • Moved the Environmental Variable selector to the Habitat Suitabilities module.
  • Rewrote the Habitat Suitability module including:
    • Removed the “Transform suitabilities using the number of Environmental Variables as the nth root on the Habitat Suitability Matrix?” option to simplify the tool.
    • Updated the Habitat Suitability Matrix output table:
      • Row names now label each combination of environmental values.
      • You can view habitat suitabilities by species in addition to guild now. Note that the numbers are different between species and guild table. The guild table takes the mean of the species in that guild, assigns a value of 1 to the highest score and each other value is divided by the maximum of their respective column. The species values are the individual habitat suitability scores divided by the sum of their respective column.
  • Know issues:
    • There seems to be a problem with the web server and VPNs. When using a VPN, the websocket sometimes closes shortly after loading the site and the site will become unresponsive and eventually grey out. To resolve the issue, reload the page.

2022-02-07

  • Added the optional ability to export a species list by copying to clipboard or downloading as a .csv file.
  • Adjusted starting view of the map to show most of Canada instead of just the Great Lakes region.
  • Fixed WebSocket time-out bug that would disconnect app after 90 seconds of inactivity.
  • Fixed bug that would crash the page if lat or long were blank.
  • Removed “There are 0 species in selected watershed” from output.

2022-02-01

  • Updated application framework using the Golem package.
  • Updated interface using Shiny Dashboard.
  • Moved code to Shiny modules.
  • Rewrote the ‘Choose fish species’ module including:
    • Implemented an updated list of species in each tertiary watershed from: Mandrak, N.E., R.A. Curry, P. Dumont, E. Holm, and D. Watkinson. (in prep). Atlas of the freshwater fishes of Canada with a taxonomic key.
    • Fixed bugs that would crash the application if certain parts of the map were clicked.
    • When using the map, there is a table output that shows the Lat, Long, Watershed ID, Drainage Area, Subdrainage Area, Tertiary Watershed Name and Number of Species at each pin.
    • Removed the “Compile species list” button. Species lists are generated automatically based on selection.
    • Updated the tertiary watershed ID selection method to include the names of the watershed. You can search by typing in the box.
    • Removed the Major Lake selection method. You can click these watersheds using the map or search for them by typing their name in the Tertiary Watershed ID box.
    • Moved ‘GIS Coordinates’ tab to ‘Map’ tab. Entered values will appear on the Leaflet map. New error handling messages will pop-up if something is wrong with the entry.

▾ Quickstart

The fish list determines which species will be included in the assessment.

To define the fish list:

  • pinpoint the assessment locations using the Select by map tab (default), or
  • select the locations by name through the Select by tertiary watershed ID tab, or
  • indicate the Area of Concern fish list to use with the Select by Area of Concern tab

If you are selecting locations using the map:

  • click on the map or enter coordinates to add locations
  • use the “Clear Locations” button to restart
  • blue pins indicate currently selected locations

To assess the fish list:

  • use the searchable fish list to see which species will be included based on your chosen location(s)
    • the list appears once at least one location is selected

Optionally:

  • click on species in the list to exclude them from the analysis
    • NOTE: species should only be excluded with justification and adjustments should be agreed upon with fisheries and fish habitat managers
  • excluded species can be returned by clicking on them again
  • copy or download fish list

Once the fish list is generated, you can move on to the next step.


▾ Quickstart

Species are grouped into guilds to help summarize the assessment results.

To group species into guilds:

  • select one or more groupings using the check boxes
  • a maximum of two selections are recommended

The following guilds are currently available:

  • adult thermal requirement (coldwater; coolwater; warmwater)
  • vegetation-association (high; low)
  • piscivory (piscivore; non-piscivore)

To assess the guilds:

  • use the histogram below to see how many species were assigned to each guild or guild grouping
  • use the table on the right to see species not assigned to any guild due to missing data
    • these species will be excluded from all further guild-level analyses

Once the guilds have been generated, you can move on to the next step.

Guilds

Missing fish

These species are missing data required to be assigned to a guild and are excluded from the model.

▾ Quickstart

A habitat suitability matrix (HSM) compiles all the available habitat preference information for the species and guilds in the assessment.

To calculate the HSM:

  • use the check boxes to select which habitat features to consider
  • click on the “Update Habitat Suitability Matrix” button to recalculate the matrix

To assess the HSM:

  • use the “HSM viewer” panel to view the generated matrix
  • use the “Missing fish” panel to identify species excluded due to missing data
  • use the radio buttons in the “Explore HSM” panel to view the data in different ways
    • use the “Explore HSM by” radio buttons to display the matrix by guild or species
    • use the “Select life stage to display” radio buttons to display the HSM and “Missing fish” table for other life stages

Once the matrix has been generated, you can move on to the next step.

Calculate habitat suitability matrix (HSM)

Explore HSM

Missing fish

HSM viewer

▾ Quickstart

A habitat scenario spreadsheet is used to describe the habitat available in the study area and how it changes between scenarios.

To prepare a habitat scenario spreadsheet:

  • use the “Download Template Spreadsheet” button to download the template habitat scenario spreadsheet (.xlsx)
    • rename the template file
    • follow the instructions in the first sheet to fill the remaining sheets
  • use the “Download Example Spreadsheet” button to download a filled example habitat scenario spreadsheet
    • the example can be used as a reference for filling the template
    • alternatively, use the example in place of your own habitat scenario spreadsheet for a non-representative trial run
  • use the “Upload Project Spreadsheet” button to upload your completed habitat scenario spreadsheet

To assess your scenarios:

  • use the viewer that appears below to view your habitat spreadsheet

Once the habitat scenario spreadsheet has been successfully uploaded, you can move on to the next step.

Project habitat information

Download habitat scenario spreadsheets

▾ Quickstart

A thermal profile spreadsheet is used to describe the how the water temperature varies by location, depth, and day of the year to asses the thermal suitability of a habitat. This step is optional.

To prepare a thermal profile spreadsheet:

  • use the “Download Template Spreadsheet” button to download the template thermal profile spreadsheet (.xlsx)
    • rename the template file
    • follow the instructions in the first sheet to fill the remaining sheets
  • use the “Download Example Spreadsheet” button to download a filled example thermal profile spreadsheet
    • the example can be used as a reference for filling the template
    • alternatively, use the example in place of your own thermal profile spreadsheet for a non-representative trial run
  • use the “Upload Project Spreadsheet” button to upload your completed habitat thermal profile spreadsheet

To assess your thermal profile:

  • use the viewer that appears below to view your thermal profile spreadsheet

Once the thermal profile spreadsheet has been successfully uploaded, you can move on to the next step.

Project thermal profile

Download thermal profile spreadsheets

Missing fish

▾ Quickstart

The weighted suitable area (WSA) summarizes the quality and area of habitat available in each scenario for each guild.

To run the WSA Analysis:

  • the app will run the analysis once you open this step
  • this can take a few minutes depending on the complexity of your scenarios and the number of included species

To assess the WSA Analysis:

  • view the summary table and plot below

Optionally:

  • return to a previous step to make any changes to the analysis
  • complete subsequent steps as needed to return here to re-run the analysis

Once you are happy with the analysis, use the “Save” button in the main menu on the left to download the full report.

WSA Summary

WSA Plot