• Arctic SDI catalogue
  •  
  •  
  •  

Shallow substrate model (20m) of the Pacific Canadian coast

The shallow substrate bottom type model was created to support near shore habitat modelling. Data sources include both available observations of bottom type and environmental predictor layers including oceanographic layers, fetch, and bathymetry and its derivatives. Using weighted random forest classification from the ranger R package, the relationship between observed bottom type and predictor layers can be determined, allowing bottom type to be classified across the study areas. The predicted raster files are classified as follows: 1) Rock, 2) Mixed, 3) Sand, 4) Mud

The categorical substrate model domains are restricted to the extent of the input bathymetry layers (see data sources) which is 5 km from the 50 m depth contour.

Simple

Date ( RI_367 )
2020-01-31
Date ( RI_366 )
2015-01-01
RI_413
  Government of Canada; Fisheries and Oceans Canada; STAR - Dr. Dana Haggarty ( Inshore Rockfish and Lingcod Program Head )
Pacific Biological Station 3190 Hammond Bay Road , Nanaimo , British Columbia , V9T 6N7 , Canada
250-756-7386
RI_415
  Government of Canada; Fisheries and Oceans Canada; Marine Spatial Ecology and Analytics Section (MSEA) - Joanne Lessard ( Research Biologist )
Pacific Biological Station 3190 Hammond Bay Road , Nanaimo , British Columbia , V9T 6N7 , Canada
250-729-8364
Credit
Du Preez, C. 2015. A new arc–chord ratio (ACR) rugosity index for quantifying three-dimensional landscape structural complexity. Landscape Ecology 30:181-192. https://link.springer.com/article/10.1007/s10980-014-0118-8.
Credit
Gregr EJ, Haggarty DR, Davies SC, Fields C, Lessard J (2021) Comprehensive marine substrate classification applied to Canada’s Pacific shelf. PLoS ONE 16(10): e0259156. https://doi.org/10.1371/journal.pone.0259156.
Credit
Masson, D., and I. Fine (2012), Modeling seasonal to interannual ocean variability of coastal British Columbia, J. Geophys. Res., 117, C10019. doi:10.1029/2012JC008151.
Credit
Soontiens, N., Allen, S., Latornell, D., Le Souef, K., Machuca, I., Paquin, J.-P., Lu, Y., Thompson, K., Korabel, V., 2016. Storm surges in the Strait of Georgia simulated with a regional model. Atmosphere-Ocean 54 1-21. https://dx.doi.org/10.1080/07055900.2015.1108899.
Status
onGoing; enContinue RI_596
Maintenance and update frequency
irregular; irrégulier RI_541
Keywords
  • Ocean bottom
  • Sea bed
  • Seabed
  • Rugosity
Government of Canada Core Subject Thesaurus Thésaurus des sujets de base du gouvernement du Canada ( RI_528 )
  • Sediments
  • Ocean floor
Classification
unclassified; nonClassifié RI_484
Use limitation
Open Government Licence - Canada (http://open.canada.ca/en/open-government-licence-canada)
Access constraints
license; licence RI_606
Use constraints
license; licence RI_606
Spatial representation type
grid; grille RI_636
Metadata language
eng; CAN
Character set
utf8; utf8 RI_458
Topic category
  • Oceans
Begin date
1984-01-01
End date
2019-12-31
N
S
E
W
thumbnail


Supplemental Information

Substrate observations were assembled from the following sources: Canadian Hydrographic Service (CHS), Dive survey data, CHS marsh data, Natural Resources Canada (NRCan), and Remotely Operated Vehicle (ROV) surveys. These observations were mapped to common bottom type classes: rock, mixed, sand, or mud.

Using ArcGIS, the points were classified into training (2/3) or testing (1/3) data. The training subset is fully withheld from the model-building process and is used to evaluate each model’s performance. The random partitioning of the data into training and test subsets does not address the issue of spatial autocorrelation between observations.

The code to create the model follows the following steps:

A raster stack of environmental predictors is created. Point observations are overlayed onto the raster stack, and the values from the predictors are extracted to the points. Records with invalid BType4 values or with NA values from the predictors are removed. The training data are weighted according to their prevalence and are used to fit a random forest model using the ranger package (which supports case weighting). The fitted model is used to predict to the extent of the input environmental raster stack, classifying the entire area into rock, mixed, sand, or mud. The predicted surface is exported as a GeoTIFF raster file in the same resolution as the raster stack predictors (in this case, 100 metre resolution) and with the same projection. Evaluation statistics including Kappa, and accuracy by predicted class are generated using the withheld test data.

Manual steps after the model has been generated:

1) Reproject layer to EPSG: 3005 (R does not support writing the top-level EPSG code to the coordinate reference system information).

2) Create a raster attribute table with SUBSTRATE field for text classes.

3) Add a field for prevalence in the raster attribute table.

The bathymetry and its derivatives were created using the Arcpy module in python (see Scripts section in the metadata). The bathymetry layer was smoothed using a focal mean prior to generating the following derivatives: slope -> standard deviation of slope, curvature, and rugosity. This step was required as a method to reduce artefacts found in the derivatives. During development, these artefacts from the non-smoothed bathymetric derivatives carried through to the predicted substrate models. The non-smoothed bathymetry was used to generate the standardized BPI layers because this processing already involves processing with a neighbourhood of cells. As input to the random forest model, the original non-smoothed bathymetry was used. Ocean energy layers were also included – mean bottom ocean currents and mean tidal speed on the bottom. The SOG region uses the Salish Sea NEMO model (Allen) as source data for the ocean energy layers. The other 4 regions are sourced the the BC ROMS model (Masson). The original data for the Regional Ocean Modeling System (ROMS) has a 3 by 3 km grid resolution. These data were interpolated using Spline with Barriers (ESRI) and resampled to 20 m resolution rasters. See the scripts section for a link to the ROMS data processing. The source data for the NEMO model had higher resolution in the Strait of Georgia and so it was decided that this model would be used for the SOG region. They were first interpolated to a 40 m cell resolution (because of computational limitations) and then resampled to 20 m. The NEMO Tidal and Circulation layers were smoothed using Focal Statistics in ArcGIS with a 13 cell neighbourhood. Fetch was also included as a predictor. Fetch points were interpolated to the extent of the raster stack (specific methods and exact source data are unclear). DFO 20 m bathymetry layers (that included terrestrial elevation data) were used as the bathymetry source. The bathymetric position index (BPI) layers were created using the Benthic Terrain Modeler toolbox and were standardized after being calculated. It is important to note that when calculating BPI, the tool expects bathymetric data to have negative values associated with depths rather than positive.

Predictor Layers:

1: Bathymetry

2: Slope (bathymetric derivative) – degrees

3: Standard Deviation of Slope (bathymetric derivative)

4: Broad Bathymetric Position Index (bathymetric derivative) - Inner Radius: 25 - Outer Radius: 250

5: Medium Bathymetric Position Index (bathymetric derivative) - Inner Radius: 10 - Outer Radius: 100

6: Fine Bathymetric Position Index (bathymetric derivative) - Inner Radius: 3 - Outer Radius: 25

7: Curvature (bathymetric derivative; slope of slope)

8: Rugosity (bathymetric derivative; Arc-Chord rugosity)

9: Circulation

10: Tidal

11: Fetch

Reference system identifier
http://www.epsg-registry.org / EPSG:3005 /
Distribution format
  • TIFF ( Unknown )

RI_412
  Government of Canada; Fisheries and Oceans Canada; Marine Spatial Ecology and Analytics Section (MSEA) - Joanne Lessard ( Research Biologist )
Pacific Biological Station 3190 Hammond Bay Road , Nanaimo , British Columbia , V9T 6N7 , Canada
250-729-8364
OnLine resource
Shallow substrate model (20m) of the Pacific Canadian coast - Tiff ( HTTPS )

Dataset;TIFF;eng,fra

OnLine resource
References ( HTTPS )

Supporting Document;PDF;eng,fra

OnLine resource
Data Dictionary ( HTTPS )

Supporting Document;CSV;eng

OnLine resource
Data Dictionary ( HTTPS )

Supporting Document;CSV;fra

OnLine resource
Shallow substrate model (20m) of the Pacific Canadian coast - GIS Hub metadata ( HTTPS )

Supporting Document;PDF;eng

OnLine resource
Shallow substrate model (20m) of the Pacific Canadian coast - GIS Hub metadata ( HTTPS )

Supporting Document;PDF;fra

OnLine resource
Shallow substrate model (20m) of the Pacific Canadian coast ( ESRI REST: Map Server )

Web Service;ESRI REST;eng

OnLine resource
Shallow substrate model (20m) of the Pacific Canadian coast ( ESRI REST: Map Server )

Web Service;ESRI REST;fra

File identifier
b100cf6c-7818-4748-9960-9eab2aa6a7a0 XML
Metadata language
eng; CAN
Character set
utf8; utf8 RI_458
Hierarchy level
dataset; jeuDonnées RI_622
Date stamp
2025-02-07T14:33:02.845Z
Metadata standard name
North American Profile of ISO 19115:2003 - Geographic information - Metadata
Metadata standard version
CAN/CGSB-171.100-2009
RI_414
  Government of Canada; Fisheries and Oceans Canada; Marine Spatial Ecology and Analytics Section (MSEA) - Joanne Lessard ( Research Biologist )
Pacific Biological Station 3190 Hammond Bay Road , Nanaimo , British Columbia , V9T 6N7 , Canada
250-729-8364
 
 

Overviews

overview
ShallowSubstrate_thumbnail.jpg

Spatial extent

N
S
E
W
thumbnail


Keywords


Provided by

logo

Associated resources

Not available


  •  
  •  
  •