DOI: 10.5061/dryad.sf7m0cgjc
title: High-resolution species distribution modelling of two coastal biogenic habitat-forming species in an Ecologically and Biologically Significant Area of the Bay of Fundy, Canada

description: High-resolution species distribution models (SDMs) were developed for two
 benthic invertebrate species of marine conservation significance across a
 113 km2 Ecologically and Biologically Significant Area (EBSA) of the Bay
 of Fundy, Canada. The stalked tunicate, Boltenia ovifera, and horse
 mussel, Modiolus modiolus, can form coastal biogenic habitat and are
 vulnerable to disturbance. A near-seabed imaging survey (depths ranging
 from 8 to 79 m) provided presence, absence, and abundance data for both
 species. Boosted Regression Tree SDMs combined these data with 11
 environmental variables. Presence-probability distributions were
 generated; however, abundance patterns could not be adequately modelled.
 Oblique geographic coordinates, which incorporate location of samples as
 information, proved useful for predicting species presence, along with
 seabed rugosity, maximum current speed and bathymetry for B. ovifera, and
 maximum and minimum current speed along with seabed rugosity for M.
 modiolus. High-resolution SDMs (in this case, 5-m grid) provide enhanced
 spatial context for ocean managers towards marine spatial planning in
 high-use coastal marine environments where bottom contact fisheries access
 and other coastal development must be balanced against marine conservation
 objectives.
description: # High-resolution species distribution modelling of two coastal biogenic
 habitat-forming species in an Ecologically and Biologically Significant
 Area of the Bay of Fundy, Canada Dataset DOI:
 [10.5061/dryad.sf7m0cgjc](10.5061/dryad.sf7m0cgjc) ## Description of the
 data and file structure There are two data files, one for each of two
 benthic invertebrates that were censused using a near-seafloor optical
 imaging system. The species are *Boltenia ovifera* (file:
 model_data_boltenia.csv) and *Modiolus modiolus* (file:
 model_data_modiolus.csv). Within each data file, the numerical count and
 presence/absence of the species is listed for each photographic image
 analyzed from the survey data set. For each station, values are provided
 for eleven different environmental variables extracted from a set of
 raster data layers that cover the survey area domain. Twenty-two raster
 layers were used in initial analyses narrowed down to 11 variables from
 multicollinearity tests. In addition to the 11 environmental variables, a
 set of 15 oblique geographic coordinate values are provided for each image
 location. The BRTmodels.R file provides the R code used to run boosted
 regression tree models with oblique geographic coordinates based on the
 .csv files. The Raster_layers.zip file provides the raster for all 22
 environmental predictors at the original 1-m resolution and resampled 5-m
 resolution, along with the final model outputs indicating the probability
 of presence and prevalence of both *Boltenia ovifera* and *Modiolus
 modiolus*. In the EnvVariables_5m folder the .tif files are accompanied by
 metadata files (.tfw,.aux,.ovr,.xml).  These 5m layers were used in final
 species distribution model iterations, so these extra files are the
 metadata (i.e., spatial statistics). With these additional files the 5m
 layers will load in a GIS environment much quicker than a standalone tif.
 ### Files and variables The variables below are defined based on file
 name.   #### File: model_data_modiolus.csv **Description:** **The count
 and presence of** ***Modiolus modiolus*** **along with derived
 environmental variable values according to an analyzed image and its
 associated location.** ##### Variables * Count: Count of the number of
 *Modiolus modiolus* observed in an image. * Presence: Presence (1) or
 absence (0) of *Modiolus modiolus* in an image. * station: Drift transect
 station number (49 transects total). * OGC1: The first oblique coordinate
 angle computed at an image location (see Møller et al. 2020 for details).
 * OGC2: The second oblique coordinate angle computed at an image location
 (see Møller et al. 2020 for details). * OGC3: The third oblique coordinate
 angle computed at an image location (see Møller et al. 2020 for details).
 * OGC4: The fourth oblique coordinate angle computed at an image location
 (see Møller et al. 2020 for details). * OGC5: The fifth oblique coordinate
 angle computed at an image location (see Møller et al. 2020 for details).
 * OGC6: The sixth oblique coordinate angle computed at an image location
 (see Møller et al. 2020 for details). * OGC7: The seventh oblique
 coordinate angle computed at an image location (see Møller et al. 2020 for
 details). * OGC8: The eighth oblique coordinate angle computed at an image
 location (see Møller et al. 2020 for details). * OGC9: The ninth oblique
 coordinate angle computed at an image location (see Møller et al. 2020 for
 details). * OGC10: The tenth oblique coordinate angle computed at an image
 location (see Møller et al. 2020 for details). * OGC11: The eleventh
 oblique coordinate angle computed at an image location (see Møller et al.
 2020 for details). * OGC12: The twelfth oblique coordinate angle computed
 at an image location (see Møller et al. 2020 for details). * OGC13: The
 thirteenth oblique coordinate angle computed at an image location (see
 Møller et al. 2020 for details). * OGC14: The fourteenth oblique
 coordinate angle computed at an image location (see Møller et al. 2020 for
 details). * OGC15: The fifteenth oblique coordinate angle computed at an
 image location (see Møller et al. 2020 for details). * Bathymetry: The
 depth value (chart datum - m) derived from the bathymetry layer at an
 image location. * Backscatter: The backscatter (db) derived from the
 backscatter layer at an image location. * Northness: The northness
 (unitless) value from the northness layer (derived from the bathymetry
 layer) at an image location. * CurrentMax: Maximum current speed (m/s)
 value at an image location. * CurrentMin: Minimum current speed (m/s)
 value at an image location. * ShoreDist: The distance from shore (m) value
 derived from coastal shapefiles at an image location.  * Habitat: Binary
 substrate classification (hard [1]/soft [0]) value derived from
 classification shapefiles (Substrate layer) at an image location. *
 RDMV: The Relative Deviation from the Mean Value (RDMV - unitless) value
 from the RDMV layer (derived from the bathymetry layer) at an image
 location. * Rugosity: The rugosity (unitless) value from the rugosity
 layer (derived from the bathymetry layer) at an image location. *
 Eastness: The eastness (unitless) value from the eastness layer (derived
 from the bathymetry layer) at an image location. * Slope: The slope
 (degrees) value from the slope layer at an image location. #### File:
 model_data_boltenia.csv **Description:** **The count and presence of**
 ***Boltenia ovifera*** **along with derived environmental variable values
 according to an analyzed image and its associated location.**  #####
 Variables * Count: Count of the number of *Boltenia ovifera* observed in
 an image. * Presence: Presence (1) or absence (0) of *Boltenia ovifera* in
 an image. * station: Drift transect station number (49 transects total). *
 OGC1: The first oblique coordinate angle computed at an image location
 (see Møller et al. 2020 for details). * OGC2: The second oblique
 coordinate angle computed at an image location (see Møller et al. 2020 for
 details). * OGC3: The third oblique coordinate angle computed at an image
 location (see Møller et al. 2020 for details). * OGC4: The fourth oblique
 coordinate angle computed at an image location (see Møller et al. 2020 for
 details). * OGC5: The fifth oblique coordinate angle computed at an image
 location (see Møller et al. 2020 for details). * OGC6: The sixth oblique
 coordinate angle computed at an image location (see Møller et al. 2020 for
 details). * OGC7: The seventh oblique coordinate angle computed at an
 image location (see Møller et al. 2020 for details). * OGC8: The eighth
 oblique coordinate angle computed at an image location (see Møller et al.
 2020 for details). * OGC9: The ninth oblique coordinate angle computed at
 an image location (see Møller et al. 2020 for details). * OGC10: The tenth
 oblique coordinate angle computed at an image location (see Møller et al.
 2020 for details). * OGC11: The eleventh oblique coordinate angle computed
 at an image location (see Møller et al. 2020 for details). * OGC12: The
 twelfth oblique coordinate angle computed at an image location (see Møller
 et al. 2020 for details). * OGC13: The thirteenth oblique coordinate angle
 computed at an image location (see Møller et al. 2020 for details). *
 OGC14: The fourteenth oblique coordinate angle computed at an image
 location (see Møller et al. 2020 for details). * OGC15: The fifteenth
 oblique coordinate angle computed at an image location (see Møller et al.
 2020 for details). * Bathymetry: The depth value (chart datum - m) derived
 from the bathymetry layer at an image location. * Backscatter: The
 backscatter (db) derived from the backscatter layer at an image location.
 * Northness: The northness (unitless) value from the northness layer
 (derived from the bathymetry layer) at an image location. *
 CurrentMax: Maximum current speed (m/s) value at an image location. *
 CurrentMin: Minimum current speed (m/s) value at an image location. *
 ShoreDist: The distance from shore (m) value derived from coastal
 shapefiles at an image location.  * Habitat: Binary substrate
 classification (hard [1]/soft [0]) value derived from classification
 shapefiles (Substrate layer) at an image location. * RDMV: The Relative
 Deviation from the Mean Value (RDMV - unitless) value from the RDMV layer
 (derived from the bathymetry layer) at an image location. * Rugosity: The
 rugosity (unitless) value from the rugosity layer (derived from the
 bathymetry layer) at an image location. * Eastness: The eastness
 (unitless) value from the eastness layer (derived from the bathymetry
 layer) at an image location. * Slope: The slope (degrees) value from the
 slope layer at an image location. #### File: BRT_models.R
 **Description:** **R file containing the R script to configure and run the
 presence probability boosted regression tree models using oblique
 geographic coordinates (OGCs, see Møller et al. 2020 for details).**  ####
 File: Raster_layers.zip **Description: Raster files (.tif) of all 22
 environmental variables used for initial species distribution modelling as
 well as the final model outputs.** Sub-file: EnvVariables_1m *
 aspect_1m.tif: The aspect (identifying the direction the downhill slope
 faces - in radians) raster layer at a 1-m spatial resolution derived from
 the bathymetry layer, clipped to the study area. * Backscatter_1m.tif: The
 backscatter (db) raster layer at a 1-m spatial resolution from the Ocean
 Mapping Group (open source), clipped to the study area. *
 Bathymetry_1m.tif: The bathymetry (m) raster layer at a 1-m spatial
 resolution from the Ocean Mapping Group (open source), clipped to the
 study area. * Bathymetry_mean_1m.tif: The mean bathymetry (neighbourhood
 size of 3x3 - in m) raster layer at a 1-m spatial resolution derived from
 the bathymetry layer, clipped to the study area. *
 Bathymetry_sd_1m.tif: The standard deviation of the bathymetry
 (neighbourhood size of 3x3 - in m) raster layer at a 1-m spatial
 resolution derived from the bathymetry layer, clipped to the study area. *
 Bathymetry_slope_1m.tif: The slope (degrees) raster layer at a 1-m spatial
 resolution derived from the bathymetry layer, clipped to the study area. *
 Cos_aspect_1m.tif: The cosine of the aspect (radians) raster layer at a
 1-m spatial resolution derived from the aspect layer, clipped to the study
 area.  * Current_max_1m.tif: The maximum current speed (m/s) raster layer
 at a 1-m spatial resolution derived from Page et al. 2015, clipped to the
 study area. * Current_mean_1m.tif: The mean current speed (m/s) raster
 layer at a 1-m spatial resolution derived from Page et al. 2015, clipped
 to the study area. * Current_min_1m.tif: The minimum current speed (m/s)
 raster layer at a 1-m spatial resolution derived from Page et al. 2015,
 clipped to the study area. * Current_sd_1m.tif: The standard deviation of
 the current speed (m/s) raster layer at a 1-m spatial resolution derived
 from Page et al. 2015, clipped to the study area. * Curvature_1m.tif: The
 curvature (pixel value) raster layer at a 1-m spatial resolution derived
 from the bathymetry layer, clipped to the study area. *
 Eastness_1m.tif: The eastness (unitless) raster layer at a 1-m spatial
 resolution derived from the bathymetry layer, clipped to the study area. *
 Northness_1m.tif: The northness (unitless) raster layer at a 1-m spatial
 resolution derived from the bathymetry layer, clipped to the study area. *
 RDMV_1m.tif: The Relative Deviation from the Mean Value (RDMV - unitless)
 raster layer at a 1-m spatial resolution derived from the bathymetry
 layer, clipped to the study area. * Roughness_1m.tif: The roughness (pixel
 value) raster layer at a 1-m spatial resolution derived from the
 backscatter layer, clipped to the study area. * Ruggedness_1m.tif: The
 ruggedness (unitless) raster layer at a 1-m spatial resolution derived
 from the bathymetry layer, clipped to the study area. *
 Rugosity_1m.tif: The rugosity (unitless) raster layer at a 1-m spatial
 resolution derived from the bathymetry layer, clipped to the study area. *
 Shore_distance_1m.tif: The distance from shore (m) raster layer at a 1-m
 spatial resolution from open-source shapefiles, clipped to the study area.
 * Sin_aspect_1m.tif: The sine of the aspect (radians) raster layer at a
 1-m spatial resolution derived from the aspect layer, clipped to the study
 area.  * Slope_1m.tif: The slope (degrees) raster layer at a 1-m spatial
 resolution from the Ocean Mapping Group (open source), clipped to the
 study area. * Substrate_1m.tif: The binary substrate classification
 (hard/soft) raster layer at a 1-m spatial resolution from open-source
 shapefiles, clipped to the study area. Sub-file: EnvVariables_5m
 (accompanied by metadata files: .tfw, .aux, .ovr, .xml) * aspect_5m.tif:
 The aspect (identifying the direction the downhill slope faces - in
 radians) raster layer at a 5-m spatial resolution derived from the
 bathymetry layer, clipped to the study area. * Backscatter_5m.tif: The
 backscatter (db) raster layer at a 5-m spatial resolution from the Ocean
 Mapping Group (open source), clipped to the study area. *
 Bathymetry_5m.tif: The bathymetry (m) raster layer at a 5-m spatial
 resolution from the Ocean Mapping Group (open source), clipped to the
 study area. * Bathymetry_mean_5m.tif: The mean bathymetry (neighbourhood
 size of 3x3 - in m) raster layer at a 5-m spatial resolution derived from
 the bathymetry layer, clipped to the study area. *
 Bathymetry_sd_5m.tif: The standard deviation of the bathymetry
 (neighbourhood size of 3x3 - in m) raster layer at a 5-m spatial
 resolution derived from the bathymetry layer, clipped to the study area. *
 Bathymetry_slope_5m.tif: The slope (degrees) raster layer at a 5-m spatial
 resolution derived from the bathymetry layer, clipped to the study area. *
 Cos_aspect_5m.tif: The cosine of the aspect (radians) raster layer at a
 5-m spatial resolution derived from the aspect layer, clipped to the study
 area.  * Current_max_5m.tif: The maximum current speed (m/s) raster layer
 at a 5-m spatial resolution derived from Page et al. 2015, clipped to the
 study area. * Current_mean_5m.tif: The mean current speed (m/s) raster
 layer at a 5-m spatial resolution derived from Page et al. 2015, clipped
 to the study area. * Current_min_5m.tif: The minimum current speed (m/s)
 raster layer at a 5-m spatial resolution derived from Page et al. 2015,
 clipped to the study area. * Current_sd_5m.tif: The standard deviation of
 the current speed (m/s) raster layer at a 5-m spatial resolution derived
 from Page et al. 2015, clipped to the study area. * Curvature_5m.tif: The
 curvature (pixel value) raster layer at a 5-m spatial resolution derived
 from the bathymetry layer, clipped to the study area. *
 Eastness_5m.tif: The eastness (unitless) raster layer at a 5-m spatial
 resolution derived from the bathymetry layer, clipped to the study area. *
 Northness_5m.tif: The northness (unitless) raster layer at a 5-m spatial
 resolution derived from the bathymetry layer, clipped to the study area. *
 RDMV_5m.tif: The Relative Deviation from the Mean Value (RDMV - unitless)
 raster layer at a 5-m spatial resolution derived from the bathymetry
 layer, clipped to the study area. * Roughness_5m.tif: The roughness (pixel
 value) raster layer at a 5-m spatial resolution derived from the
 backscatter layer, clipped to the study area. * Ruggedness_5m.tif: The
 ruggedness (unitless) raster layer at a 5-m spatial resolution derived
 from the bathymetry layer, clipped to the study area. *
 Rugosity_5m.tif: The rugosity (unitless) raster layer at a 5-m spatial
 resolution derived from the bathymetry layer, clipped to the study area. *
 Shore_distance_5m.tif: The distance from shore (m) raster layer at a 5-m
 spatial resolution from open-source shapefiles, clipped to the study area.
 * Sin_aspect_5m.tif: The sine of the aspect (radians) raster layer at a
 5-m spatial resolution derived from the aspect layer, clipped to the study
 area.  * Slope_5m.tif: The slope (degrees) raster layer at a 5-m spatial
 resolution from the Ocean Mapping Group (open source), clipped to the
 study area. * Substrate_5m.tif: The binary substrate classification
 (hard/soft) raster layer at a 5-m spatial resolution from open-source
 shapefiles, clipped to the study area. Sub-file: Model_outputs *
 boltenia_brt_ogc16_prob.tif: The probability of presence (ranging from
 0-1) species distribution model output raster layer of *Boltenia
 ovifera* at a 5-m spatial resolution. * boltenia_brt_prevalence.tif: The
 prevalence (present/absent) species distribution model output raster layer
 of *Boltenia ovifera* at a 5-m spatial resolution. *
 modiolus_brt_ogc16_prob.tif: The probability of presence (ranging from
 0-1) species distribution model output raster layer of *Modiolus modiolus*
 at a 5-m spatial resolution. * modiolus_brt_prevalence.tif: The prevalence
 (present/absent) species distribution model output raster layer
 of *Modiolus modiolus* at a 5-m spatial resolution. ## Code/software The
 file BRT_models.R contains the code for both species' distribution
 models. ## Access information Other publicly accessible locations of the
 species data: *
 [https://open.canada.ca/data/en/dataset/152ae3f1-d2b9-43d9-a7b4-d769d9e9fc41](https://open.canada.ca/data/en/dataset/152ae3f1-d2b9-43d9-a7b4-d769d9e9fc41)  Data was derived from the following sources: * [http://omg.unb.ca/projects/South_West_NB/html/](http://omg.unb.ca/projects/South_West_NB/html/) * [https://search.open.canada.ca/openmap/f2c493e4-ceaa-11eb-be59-1860247f53e3](https://search.open.canada.ca/openmap/f2c493e4-ceaa-11eb-be59-1860247f53e3) * [http://www.snb.ca/geonb1/e/DC/catalogue-E.asp](http://www.snb.ca/geonb1/e/DC/catalogue-E.asp) * Page, F. H., Losier, R., Haigh, S., Bakker, J., Chang, B. D., McCurdy, P., Beattie, M., *et al.* 2015. Transport and dispersal of sea lice bath therapeutants from salmon farm net-pens and well-boats. DFO Can. Sci. Advis. Sec. Res. Doc. 2015/064. xviii +148 p. Oblique geographic coordinates source: * Møller, A. B., Beucher, A. M., Pouladi, N., and Greve, M. H. 2020. Oblique geographic coordinates as covariates for digital soil mapping. SOIL 6, 269–289. [https://doi.org/10.5194/soil-6-269-2020](https://doi.org/10.5194/soil-6-269-2020).