Marine bird density and distribution on Canada's Pacific coast, 2005-2008

Caroline Fox1, OBIS-SEAMAP2

1 Dalhousie University, ; 2 Marine Geospatial Ecology Lab, Duke University, A328 LSRC building, 27708, Durham, United States

Corresponding author(s): Caroline Fox (carolinehfox@gmail.com), OBIS-SEAMAP (seamap-contact@duke.edu)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

Fox, CH, Huettmann, F, Harvey, GKA, Morgan, KH, Robinson, J, Williams, R, Paquet, PC. 2017. Predictions from machine learning ensembles: marine bird distribution and density on Canada’s Pacific coast. Marine Ecology Progress Series. 566:199-216. http://www.int-res.com/articles/meps_oa/m566p199.pdf

Abstract

Original provider:
Caroline Fox, Dalhousie University and Raincoast Conservation Foundation

Dataset credits:
Caroline Fox, Dalhousie University and Raincoast Conservation Foundation

Abstract:
Associated publication abstract: Increasingly disrupted and altered, the world’s oceans are subject to immense and intensifying anthropogenic pressures. Of the biota inhabiting these ecosystems, marine birds are among the most threatened. For conservation efforts targeting marine birds to be effective, quantitative information relating to their at-sea density and distribution is typically a crucial knowledge component. In this study, we generated predictive machine learning ensemble models for 13 marine bird species and 7 groups (representing 24 additional species) in Canada’s Pacific coast waters, including several species listed under Canada’s Species at Risk Act. Predictive models were based on systematic marine bird line transect survey information collected in spring, summer, and fall on Canada’s Pacific coast (2005−2008). Multiple Covariate Distance Sampling (MCDS) was used to estimate marine bird density along transect segments. Spatial and temporal environmental predictors, including remote sensing information, were used in model ensembles, which were constructed using 4 machine learning algorithms in Salford Systems Predictive Modeler v7.0 (SPM7): Random Forests, TreeNet, Multivariate Adaptive Regression Splines, and Classification and Regression Trees. Predictive models were subsequently combined to generate seasonal and overall predictions of areas important to marine birds based on normalized marine bird species or group richness and densities. Our results employ open access data sharing and are intended to better inform marine bird conservation efforts and management planning on Canada’s Pacific coast and for broader-scale geographic initiatives across North America and elsewhere.

Supplemental information:
Marine bird line-transect survey information collected using Distance Sampling in coastal British Columbia, Canada (2005-2008) is provided in three forms: (1) raw, unadjusted marine bird sightings; (2) for a subset of species, marine bird density estimates along 1km transect segments using Multiple Covariates Distance Sampling (MCDS), and; (3) for a subset of species, surface density estimates per ~14km2 hexagon using machine learning ensemble modeling. For data products 2 and 3, the marine bird subsets were restricted to species sighted in sufficient numbers for analysis. Surveys were completed by Raincoast Conservation Foundation.

1. Raw data: raw, unadjusted sighting of marine bird species on water and in flight. Attributes such as column labels are included in the attributes definition section. 

Note that several species alpha codes are non-standard, due to grouping of species identifications (e.g., large gulls and dark shearwaters).

ANMU = Ancient Murrelet
ANMUf = Ancient Murrelet family (varying #s of parents and chicks, or just chicks)
BAEA = Bald Eagle
BEKI = Belted Kingfisher
BFAL = Black-footed Albatross
BLKI  = Black-legged Kittiwake
BLOY = Black Oystercatcher
BLSC = Black Scoter
BLTU = Black Turnstone
BOGU = Bonaparte's Gull
BRAC = Brandt's Cormorant
BRAN = Brant Goose
BUFF = Bufflehead Duck
BULS  = Buller's Shearwater
CAAU = Cassin's Auklet
CAGU = California Gull
CANG  = Canada Goose
COLO = Common Loon
COME = Common Merganser
COMU = Common Murre
COMUf = Common Murre family (parent with chick, or just chicks)
CORA = Common Raven
DARK = Sooty Shearwater, Short-tailed Shearwater, Flesh-footed Shearwater
DCCO  = Double-crested Cormorant
DEJU = Dark-eyed Junco
DUNL = Dunlin
FTSP = Fork-tailed Storm Petrel
GBHE = Great Blue Heron
GWGU = Glaucous-winged Gull
HADU = Harlequin Duck
HETHGU = Herring Gull/Thayer's Gull
HOGR = Horned Grebe
HOPU = Horned Puffin
LAAL = Laysan Albatross
LEFTSP = mixed flock Fork-tailed and Leach's Storm-petrels
LESP = Leach's Storm Petrel
LTDU = Longtail Duck
LTJA = Long-tailed Jaeger
MALL = Mallard Duck
MAMU = Marbled Murrelet
MEGU = Mew Gull
NOCR = Northwestern Crow
NOFU = Northern Fulmar
NSHO = Northern Shoveler
OSPR = Osprey
PAJA = Parasitic Jaeger
PALO = Pacific Loon
PECO = Pelagic Cormorant
PFSH = Pink-footed Shearwater
PIGU = Pigeon Guillemot
POJA = Pomarine Jaeger
RBME = Red-breasted Merganser
RHAU = Rhinoceros Auklet
RNGR = Red-necked Grebe
RNPH = Red-necked Phalarope
RTLO = Red-throated Loon
RUHU = Rufous Hummingbird
SAGU = Sabine's Gull
SNGO = Snow Goose
STAL = Short-tailed Albatross
SUSC = Surf Scoter
THGU = Thayer's Gull
TOWA = Townsend's Warbler
TRES = Tree Swallow
TUPU = Tufted Puffin
TUPUf = Tufted Puffin family (parent with chick)
WEGR = Western Grebe
WEGU = Western Gull
WHIM = Whimbrel
WWSC = White-winged Scoter
YBLO = Yellow-billed Loon

UNAL = Unidentified Alcid 		
UNCO = Unidentified cormorant	
UNDU = Unidentified ducks in the distance	
UNGE = Unidentified Geese in the distance	
UNGO = Unidentified Goldeneye 	
UNGR = Unidentified Grebe	
ULGU = Unidentified Larus Gull 	
UNJA = Unidentified Jaeger	
UNLO = Unidentified Loon 	
UNSO = Unidentified Scoter	
UNSW = Unidentified Shearwater	
UNSH = Unidentified Shorebirds	
UNST = Unidentified Storm-petrel	
UNTE = Unidentified Tern	
UNTU = Unidentified Turnstone

2. Marine bird density estimates along 1km transect segments using Multiple Covariates Distance Sampling (MCDS). 

Note that several species alpha codes are non-standard, due to grouping of species identifications (e.g., large gulls and dark shearwaters).

ANMU = Ancient Murrelet
BFAL = Black-footed Albatross
CAAU = Cassin's Auklet
COMU = Common Murre
CORM = Cormorants (Brandt's, Double-crested, Pelagic)
DARK = Dark shearwaters (Flesh-footed, Short-tailed, Sooty)
FTSP = Fork-tailed Storm-petrel
GREB = Grebes (Horned, Red-necked, Western)
LESP = Leach's Storm-petrel
lgGULL = large Larus spp. gulls (California, Glaucous-winged, American, Thayer's)
LOON = Loons (Yellow-billed, Common, Red-throated, Pacific)
MAMU = Marbled Murrelet
NOFU = Northern Fulmar
PFSH = Pink-footed Shearwater
PIGU = Pigeon Guillemot
RHAU = Rhinoceros Auklet
RNPH = Red=necked Phalarope
SCOT = Scoters (Black, White-winged, Surf)
smGULL = small gulls (Black-legged Kittiwake, Bonaparte's, Mew, Sabine's)
TUPU = Tufted Puffin

Field names represent, using ANMU and BFAL as the examples: 

- first few fields represent summary fields (i.e., FID, Shape)
- SEGID = unique line transect segment ID. Can use this field to join across species files.
- VOYAGE = On planned transect (T) or on passage (P), which are unplanned transects.
- SPEED = vessel speed (knts).
- MO = Month, numeric (1-12).
- SegLength = Segment length. Most should = 1 km, but shorter segments have been retained.
- Season = Spring (april, may, june), Summer (August), Fall (October, November).
- Point_X and Point_Y = x and y coordinates using BC Albers.
- Effort = Same as SegLength.
- DATE = year-month-day.
- YEAR = year.
- DAY_YR = Day of the year, beginning with with January 1 = 1.
- AREA = Segment length (km) X perpendicular distance (km) from boat for that particular species (unit = km2; identified using MCDS Distance Analysis).
- ANMUw_D (all other examples BIRDw_D) = estimated density of Ancient Murrelets along the transect segment (including family groups, see below). Lowercase "w" = birds on water. 
- ANMUf_D = exception for ANMU family groups. Lowercase "f" = family groups on water (parent(s) with flightless chicks or flightless chicks alone).
- BFALs_D (all other examples BIRDs_D) = estimated density of Black-footed ALbatrosses along the transect segment. Lowercase "s" = birds in flight. Note that flying bird density estimates should be used and interpreted with caution. 

3. Density estimations per hexagon (approx. 14km2):

Shape file name represents the bird species (e.g., ANMU = Ancient Murrelet) plus "w" (w = density estimates of birds on water only) or "sw" (sw = density estimates of combination of birds in flight and on water).

Note that several species alpha codes are non-standard, due to grouping of species identifications (e.g., large gulls and dark shearwaters).

ANMU = Ancient Murrelet
BFAL = Black-footed Albatross
CAAU = Cassin's Auklet
COMU = Common Murre
CORM = Cormorants (Brandt's, Double-crested, Pelagic)
DARK = Dark shearwaters (Flesh-footed, Short-tailed, Sooty)
FTSP = Fork-tailed Storm-petrel
GREB = Grebes (Horned, Red-necked, Western)
LESP = Leach's Storm-petrel
lgGULL = large Larus spp. gulls (California, Glaucous-winged, American, Thayer's)
LOON = Loons (Yellow-billed, Common, Red-throated, Pacific)
MAMU = Marbled Murrelet
NOFU = Northern Fulmar
PFSH = Pink-footed Shearwater
PIGU = Pigeon Guillemot
RHAU = Rhinoceros Auklet
RNPH = Red=necked Phalarope
SCOT = Scoters (Black, White-winged, Surf)
smGULL = small gulls (Black-legged Kittiwake, Bonaparte's, Mew, Sabine's)
TUPU = Tufted Puffin

Field names represent, using ANMUw as the example: 

- first few ields represent summary fields (i.e., FID, Shape and Id)
- HexagonID = unique hexagon cell ID. Can use this field to join across species files.
- X_coord and Y_Coord = should be self explanatory. 
- spr_ANMUw = estimated Ancient Murrelet on water density estimates (birds/km2) in spring (April 2007, May 2007, June 2008)
- sum_ANMUw = same as above, except in summer (August 2005, 2006 and 2008)
- fal_ANMUw = same as above, except in fall (October and November 2007)
- ANMUw_AnAv = average across spring, summer, and fall density estimates

Keywords: Occurrence,Marine Animal Survey,Marine Biology,Seabirds,Visual Sighting,Vessel, Observation, Occurrence

General description

Purpose: Not available
Additional information: marine, harvested by iOBIS

Project details

Project title: Marine bird density and distribution on Canada's Pacific coast, 2005-2008
Personnel: Caroline Fox
Funding: NA

Data published through GBIF: http://ipt.env.duke.edu/resource?r=zd_1458

Taxonomic coverage

General taxonomic coverage description: Scientific names are based on the Integrated Taxonomic Information System (ITIS).
Taxonomic ranks
Order: Charadriiformes
Family: Alcidae, Anatidae, Anatidae, Podicipedidae, Gaviidae, Procellariidae, Procellariidae, Laridae
Genus: Puffinus, Histrionicus, Larus, Oceanodroma, Pandion, Larus, Phalacrocorax, Bucephala, Stercorarius, Melanitta, Arenaria
Species: Synthliboramphus antiquus, Synthliboramphus antiquus, Haliaeetus leucocephalus, Megaceryle torquata, Phoebastria nigripes, Rissa tridactyla, Haematopus bachmani, Melanitta nigra, Arenaria melanocephala, Chroicocephalus philadelphia, Phalacrocorax penicillatus, Branta bernicla, Bucephala albeola, Puffinus bulleri, Ptychoramphus aleuticus, Larus californicus, Branta canadensis, Gavia immer, Mergus merganser, Uria aalge, Uria aalge, Corvus corax, Phalacrocorax auritus, Junco hyemalis, Calidris alpina, Oceanodroma furcata, Ardea herodias, Larus glaucescens, Podiceps auritus, Fratercula corniculata, Phoebastria immutabilis, Oceanodroma leucorhoa, Clangula hyemalis, Stercorarius longicaudus, Anas platyrhynchos, Brachyramphus marmoratus, Larus canus, Corvus caurinus, Fulmarus glacialis, Anas clypeata, Stercorarius parasiticus, Gavia pacifica, Phalacrocorax pelagicus, Puffinus creatopus, Cepphus columba, Stercorarius pomarinus, Mergus serrator, Cerorhinca monocerata, Podiceps grisegena, Phalaropus lobatus, Gavia stellata, Selasphorus rufus, Xema sabini, Chen caerulescens, Phoebastria albatrus, Melanitta perspicillata, Setophaga townsendi, Fratercula cirrhata, Fratercula cirrhata, Aechmophorus occidentalis, Numenius phaeopus, Melanitta fusca, Gavia adamsii
Common names: Ancient Murrelet, Ancient Murrelet, Bald Eagle, Ringed Kingfisher, Black-footed Albatross, Black-legged Kittiwake, Black Oystercatcher, Black Scoter, Black Turnstone, Bonaparte's Gull, Brandt's Cormorant, Brant, Bufflehead, Buller's Shearwater, Cassin's Auklet, California Gull, Canada Goose, Common Loon, Common Merganser, Common Murre, Common Murre, Common Raven, Double-crested Cormorant, Dark-eyed Junco, Dunlin, Fork-tailed Storm Petrel, Great Blue Heron, Glaucous-winged Gull, Harlequin Ducks, Horned Grebe, Horned Puffin, Laysan Albatross, Dark Storm Petrels, Leach's Storm Petrel, Long-tailed Duck, Long-tailed Jaeger, Mallard, Marbled Murrelet, Mew Gull, Northwestern Crow, Northern Fulmar, Northern Shoveler, Ospreys, Parasitic Jaeger, Pacific Loon, Pelagic Cormorant, Pink-footed Shearwater, Pigeon Guillemot, Pomarine Jaeger, Red-breasted Merganser, Rhinoceros Auklet, Red-necked Grebe, Red-necked Phalarope, Red-throated Loon, Rufous Hummingbird, Sabine's Gull, Blue Goose, Short-tailed Albatross, Surf Scoter, Townsend's Warbler, Tufted Puffin, Tufted Puffin, Ducks, Ducks, Goldeneyes, Divers, Scoters, Fulmars, Fulmars, Gulls, Western Grebe, Whimbrel, Velvet Scoter, Yellow-billed Loon

Spatial coverage

General spatial coverage: British Columbia,Canada
Coordinates: 50°33'32.4''N and 54°42'43.2''N Latitude; 133°4'30''W and 126°46'33.6''W Longitude 

Temporal coverage: August 5, 2005 - August 29, 2008

Natural collections description

Parent collection identifier: OBIS-SEAMAP
Collection name: zd_1458
Collection identifier: zd_1458

Methods

Method step description: NA
Study extent description: NA
Sampling description: NA

Datasets

Dataset description
Object name: Darwin Core Archive Marine bird density and distribution on Canada's Pacific coast, 2005-2008
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: http://ipt.env.duke.edu/archive.do?r=zd_1458
Publication date of data: 2021-04-24
Language: English
Licences of use: Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0 License

External datasets

Dataset description
Object name: OBIS-SEAMAP Dataset Page
Character encoding: UTF-8
Format name: Interactive map
Distribution: http://seamap.env.duke.edu/dataset/1458

Dataset description
Object name: FGDC Metadata
Character encoding: UTF-8
Format name: XML
Distribution: http://seamap.env.duke.edu/dataset/1458/xml

Metadata language: English
Date of metadata creation: 2014-06-17
Hierarchy level: Dataset