Tall Sea Pens--Santa Barbara Channel, California

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Metadata:

Identification_Information:
Citation:
Citation_Information:
Originator: Lisa M. Krigsman
Originator: Mary M. Yoklavich
Originator: Guy R. Cochrane
Originator: Nadine E. Golden
Publication_Date: 2013
Title: Tall Sea Pens--Santa Barbara Channel, California
Geospatial_Data_Presentation_Form: GeoTIFF
Series_Information:
Series_Name: Data Series
Issue_Identification: DS 781
Publication_Information:
Publication_Place: Reston, VA
Publisher: U.S. Geological Survey
Online_Linkage: https://doi.org/10.3133/ds781
Online_Linkage: Larger_Work_Citation:
Citation_Information:
Originator: Nadine E. Golden
Publication_Date: 2013
Title: California State Waters Map Series Data Catalog
Geospatial_Data_Presentation_Form: database
Series_Information:
Series_Name: Data Series
Issue_Identification: DS 781
Publication_Information:
Publication_Place: Reston, VA
Publisher: U.S. Geological Survey
Online_Linkage: https://doi.org/10.3133/ds781
Description:
Abstract:
This part of DS 781 presents data for the map showing the predicted distribution of tall sea pens in the Santa Barbara Channel, California, region. The raster data file is included in "TallSeaPens_SantaBarbaraChannel.zip," which is accessible from https://pubs.usgs.gov/ds/781/SantaBarbaraChannel/data_catalog_SantaBarbaraChannel.html.
Presence-absence data of benthic macro-invertebrates and associated habitat (that is, sediment type and depth) were collected using a towed camera sled in selected areas along the coast off southern California during a ground-truth observation cruise conducted by the U.S. Geological Survey and NOAA National Marine Fisheries Service for the California Seafloor Mapping Program. Benthic community structure was determined from 35 video towed-camera transects within California's State Waters 3-nautical-mile limit in the Santa Barbara Channel. These transects produced a total of 923 10-second observations from the Offshore of Refugio Beach map area (34.5 degrees N., 120.1 degrees W.) to the Hueneme Canyon and vicinity map area (34.1 degrees N., 119.2 degrees W.).
Presence-absence data were collected for 29 benthic, structure-forming nonmobile taxa. Using this information, generalized linear models (GLMs) were developed to predict the probability of occurrence of five commonly observed taxa (cup corals, hydroids, short and tall sea pens, and brittle stars in the sediment) in five map areas within the Santa Barbara Channel (SBC). A sixth map area (Offshore of Carpinteria) was not modeled owing to insufficient data.
The analysis demonstrates that the community structure for the five map areas can be divided into three statistically distinct groups: (1) the Hueneme Canyon and vicinity and the Offshore of Ventura map areas; (2) the Offshore of Santa Barbara and the Offshore of Coal Oil Point map areas; and (3) the Offshore of Refugio Beach map area. These three distinct groups are the main reason that the probability for each taxa can be so dramatically different within one predictive-distribution map area. The five most frequently observed benthic macro-invertebrate taxa were selected for these predictive-distribution grids. Presence-absence data for each selected invertebrate were fit to specific generalized linear models using geographic location, depth, and seafloor character as covariates. Data for the covariates were informed by the bathymetry, seafloor character, and other ground-truth data from the different map areas of the Santa Barbara Channel region that are part of the California State Waters Map Series DS 781.
Observations based on depth were limited by the capability of the towed camera sled; as a result, no predictions were made below depths of 150 m (in other words, on the continental slope or in Hueneme Canyon). Cup corals and hydroids had high predicted probabilities of occurrence in areas of hard substrata, whereas short and tall sea pens were predicted to occur in parts of the SBC that had unconsolidated and mixed sediment. Our model predicted that brittle stars would occur throughout the entire SBC on various bottom types.
Purpose:
These data are intended for science researchers, students, policy makers, and the general public. The data can be used with geographic information systems (GIS) software to display oceanographic information.
Supplemental_Information:
Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government.
Although this Federal Geographic Data Committee-compliant metadata file is intended to document the data set in nonproprietary form, as well as in Esri format, this metadata file may include some Esri-specific terminology.
Time_Period_of_Content:
Time_Period_Information:
Range_of_Dates/Times:
Beginning_Date: 2005
Ending_Date: 2009
Currentness_Reference: ground condition
Status:
Progress: Complete
Maintenance_and_Update_Frequency: As needed
Spatial_Domain:
Bounding_Coordinates:
West_Bounding_Coordinate: -119.643628
East_Bounding_Coordinate: -119.471725
North_Bounding_Coordinate: 34.390598
South_Bounding_Coordinate: 34.320467
Keywords:
Theme:
Theme_Keyword_Thesaurus: USGS Metadata Identifier
Theme_Keyword: USGS:35f550ac-47ee-4f17-814c-b8f245e14005
Theme:
Theme_Keyword_Thesaurus: Global Change Master Directory (GCMD)
Theme_Keyword: Marine Habitat
Theme:
Theme_Keyword_Thesaurus: ISO 19115 Topic Category
Theme_Keyword: biota
Theme_Keyword: oceans
Theme:
Theme_Keyword_Thesaurus: USGS Thesaurus
Theme_Keyword: remote sensing
Theme_Keyword: modeling
Theme_Keyword: geospatial datasets
Theme_Keyword: benthos
Theme:
Theme_Keyword_Thesaurus: None
Theme_Keyword: biological prediction
Theme_Keyword: fisheries
Theme_Keyword: ecosystem
Theme_Keyword: U.S. Geological Survey
Theme_Keyword: USGS
Theme_Keyword: Coastal and Marine Hazards and Resources Program
Theme_Keyword: CMHRP
Theme_Keyword: Pacific Coastal and Marine Science Center
Theme_Keyword: PCMSC
Place:
Place_Keyword_Thesaurus: Geographic Names Information System (GNIS)
Place_Keyword: Pacific Ocean
Place_Keyword: California
Place_Keyword: Santa Barbara Channel
Place_Keyword: Hueneme Canyon
Place_Keyword: Ventura
Place_Keyword: Santa Barbara
Place_Keyword: Coal Oil Point
Place_Keyword: Refugio Beach
Access_Constraints: None
Use_Constraints:
USGS-authored or produced data and information are in the public domain from the U.S. Government and are freely redistributable with proper metadata and source attribution. Please recognize and acknowledge the U.S. Geological Survey and NOAA National Marine Fisheries as the originator(s) of the dataset and in products derived from these data. This information is not intended for navigation purposes.
Point_of_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Person: PCMSC Science Data Coordinator
Contact_Address:
Address_Type: mailing and physical
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060-5792
Country: US
Contact_Voice_Telephone: 831-427-4747
Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov
Browse_Graphic:
Browse_Graphic_File_Name: Browse_Graphic_File_Description:
Map of predicted distribution of tall sea pens in the Santa Barbara Channel region.
Browse_Graphic_File_Type: JPEG
Data_Set_Credit:
The authors would like to thank E.J. Dick (Fisheries Ecology Division, Southwest Fisheries Science Center, Santa Cruz, CA). He was a critical partner in the development of the predictive models used in this study.
Native_Data_Set_Environment:
Microsoft Windows XP Version 5.1 (Build 2600) Service Pack 3 ESRI ArcCatalog 9.3.1.3500
Cross_Reference:
Citation_Information:
Originator: Samuel Y. Johnson
Originator: Peter Dartnell
Originator: Guy R. Cochrane
Originator: Nadine E. Golden
Originator: Eleyne L. Phillips
Originator: Andrew C. Ritchie
Originator: Rikk G. Kvitek
Originator: H. Gary Greeene
Originator: Lisa M. Krigsman
Originator: Charles A. Endris
Originator: Kevin B. Clahan
Originator: Ray W. Sliter
Originator: Florence L. Wong
Originator: Mary M. Yoklavich
Originator: William R. Normark
Publication_Date: 2012
Title:
California State Waters Map Series--Hueneme Canyon and Vicinity, California
Geospatial_Data_Presentation_Form: pamphlet and map sheets
Series_Information:
Series_Name: Scientific Investigations Map
Issue_Identification: 3225
Publication_Information:
Publication_Place: Reston, VA
Publisher: U.S. Geological Survey
Online_Linkage: https://doi.org/10.3133/sim3225
Data_Quality_Information:
Attribute_Accuracy:
Attribute_Accuracy_Report: Pixel resolution 2 m.
Logical_Consistency_Report: Logical Consistency untested.
Completeness_Report:
Please see SIM pamphlet, chapter 5, for information about omissions, selection criteria, generalization, definitions used, and other rules used to derive the data set.
Positional_Accuracy:
Horizontal_Positional_Accuracy:
Horizontal_Positional_Accuracy_Report: On the order of 10 meters.
Lineage:
Process_Step:
Process_Description:
The seafloor-character map, GLMs, and the Marine Geospatial Ecology Tool (MGET; http://mgel.env.duke.edu) in ArcGIS were used to develop predictive-probability maps of occurrence per 12 sq m of seafloor for selected invertebrate taxa. The 12 sq m area was calculated by multiplying the average width of the video images by the average distance covered during the 10-second samples. The seafloor-character map provided the habitat-class data.

  tall sea pen
  taxa~Class + Depth + I(Depth^2) + Block + Class:Depth + Depth:Block, # Class + Depth + I(Depth^2) + Block + Class:Depth + Depth:Block tryCatch(taxa39.glm <- glm(taxa~Class + Depth + I(Depth^2) + Block + Class:Depth + Depth:Block, family=binomial(link="logit"), data=taxa.df),
          warning = function(x) { output.df[39,"flag"] <<- 1 },
          finally = taxa39.glm <- glm(taxa~Class + Depth + I(Depth^2) + Block + Class:Depth + Depth:Block, family=binomial(link="logit"),
  data=taxa.df)
          )
  summary(taxa39.glm)

  MODEL SUMMARY:
  ==============

  Call:
  glm(formula = sea_whip ~ factor(Class) + Depth + I(Depth^2) + factor(Block) + factor(Class):Depth + Depth:factor(Block), family = binomial(link="logit"), data = na.omit(d))

  Deviance Residuals:
      Min       1Q   Median       3Q      Max
  -2.6752  -0.4688   0.2572   0.7440   2.4073

  Coefficients:
                         Estimate Std. Error z value Pr(>|z|)
  (Intercept)          -6.5020723  0.8018151  -8.109 5.10e-16 ***
  factor(Class)2        1.1795472  1.0172347   1.160 0.246227
  factor(Class)3        2.0205740  1.4088511   1.434 0.151515
  Depth                 0.1701365  0.0217273   7.831 4.86e-15 ***
  I(Depth^2)           -0.0006330  0.0001684  -3.759 0.000171 ***
  factor(Block)2        2.1135103  0.7460851   2.833 0.004614 **
  factor(Block)3        0.5578155  0.9309282   0.599 0.549037
  factor(Class)2:Depth -0.0228452  0.0141944  -1.609 0.107518
  factor(Class)3:Depth -0.0796149  0.0216159  -3.683 0.000230 ***
  Depth:factor(Block)2 -0.0528564  0.0118935  -4.444 8.83e-06 ***
  Depth:factor(Block)3 -0.0458373  0.0162593  -2.819 0.004815 **
  ---
  Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

  (Dispersion parameter for binomial family taken to be 1)

      Null deviance: 1277.16  on 922  degrees of freedom
  Residual deviance:  724.72  on 912  degrees of freedom
  AIC: 746.72

  Number of Fisher Scoring iterations: 6

  Analysis of Deviance Table

  Model: binomial, link: logit

  Response: sea_whip

  Terms added sequentially (first to last)


                       Df Deviance Resid. Df Resid. Dev
  NULL                                   922    1277.16
  factor(Class)         2    52.31       920    1224.84
  Depth                 1   391.71       919     833.13
  I(Depth^2)            1    33.91       918     799.22
  factor(Block)         2    41.53       916     757.70
  factor(Class):Depth   2    10.41       914     747.29
  Depth:factor(Block)   2    22.57       912     724.72
 resample to 10 meters
Krigsman, L.M., M.M. Yoklavich, E.J. Dick, and G.R. Cochrane (2012) Models and maps: predicting the distribution of corals and other benthic macro-invertebrates in shelf habitats. Ecosphere 3:1-16.
Process_Date: 2010
Process_Step:
Process_Description:
Metadata was modified to bring up to current USGS PCMSC standards. USGS Thesaurus and keywords were added, and added keywords section with USGS persistent identifier as theme keyword. Information about the data available for download and different Network Resource Name links and details were given in the Standard Order Process section. Minor typos were corrected. No data information was changed. The metadata available from a harvester may supersede metadata bundled within a download file. Users are advised to compare the metadata dates to determine which metadata file is most recent.
Process_Date: 20230501
Process_Contact:
Contact_Information:
Contact_Person_Primary:
Contact_Person: Susan A Cochran
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Position: Geologist
Contact_Address:
Address_Type: mailing and physical address
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060-5792
Country: USA
Contact_Voice_Telephone: (831) 460-7545
Contact_Electronic_Mail_Address: scochran@usgs.gov
Spatial_Data_Organization_Information:
Direct_Spatial_Reference_Method: Raster
Raster_Object_Information:
Raster_Object_Type: Pixel
Row_Count: 23905
Column_Count: 47950
Vertical_Count: 1
Spatial_Reference_Information:
Horizontal_Coordinate_System_Definition:
Planar:
Map_Projection:
Map_Projection_Name: WGS 1984 UTM Zone 11N
Transverse_Mercator:
Scale_Factor_at_Central_Meridian: 0.9996
Longitude_of_Central_Meridian: -117.0
Latitude_of_Projection_Origin: 0.0
False_Easting: 500000.0
False_Northing: 0.0
Planar_Coordinate_Information:
Planar_Coordinate_Encoding_Method: coordinate pair
Coordinate_Representation:
Abscissa_Resolution: 0.000000002220024164500956
Ordinate_Resolution: 0.000000002220024164500956
Planar_Distance_Units: Meter
Geodetic_Model:
Horizontal_Datum_Name: D WGS 1984
Ellipsoid_Name: WGS 1984
Semi-major_Axis: 6378137.0
Denominator_of_Flattening_Ratio: 298.257223563
Entity_and_Attribute_Information:
Detailed_Description:
Entity_Type:
Entity_Type_Label: tallseapeans
Entity_Type_Definition:
The raster attributes include VALUE - code for the Predicted-Distribution of Tall Sea Pens for Santa Barbara Channel Region and COUNT - number of pixels.
Entity_Type_Definition_Source: ESRI
Attribute:
Attribute_Label: Rowid
Attribute_Definition: Internal feature number.
Attribute_Definition_Source: ESRI
Attribute_Domain_Values:
Unrepresentable_Domain:
Sequential unique whole numbers that are automatically generated.
Attribute:
Attribute_Label: VALUE
Attribute_Definition:
VALUE - code for the Predicted-Distribution of Tall Sea Pens for Santa Barbara Channel Region
Attribute_Definition_Source: USGS
Attribute_Domain_Values:
Range_Domain:
Range_Domain_Minimum: 2.22045e-016
Range_Domain_Maximum: .705603
Attribute:
Attribute_Label: COUNT
Attribute_Definition:
The number of pixels (2 m x 2 m size grid cell) represented in each probability raster (see Attribute: VALUE).
Attribute_Definition_Source: ESRI
Attribute_Domain_Values:
Unrepresentable_Domain:
Sequential unique whole numbers that are automatically generated.
Distribution_Information:
Distributor:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization: U.S. Geological Survey
Contact_Address:
Address_Type: mailing and physical address
Address: 345 Middlefield Rd
City: Menlo Park
State_or_Province: CA
Postal_Code: 94025-3561
Country: USA
Contact_Voice_Telephone: (650) 329-4309
Resource_Description:
The .zip file includes the .lyr, .tfw, .tif, .tif.aux.xml, and .tif.ovr files, as well as FGDC-compliant metadata.
Distribution_Liability:
Unless otherwise stated, all data, metadata and related materials are considered to satisfy the quality standards relative to the purpose for which the data were collected. Although these data and associated metadata have been reviewed for accuracy and completeness and approved for release by the U.S. Geological Survey (USGS), no warranty expressed or implied is made regarding the display or utility of the data on any other system or for general or scientific purposes, nor shall the act of distribution constitute any such warranty.
Standard_Order_Process:
Digital_Form:
Digital_Transfer_Information:
Format_Name: TIFF
Format_Version_Number: 9.3.1
Format_Specification: Arcinfo grid
File_Decompression_Technique: windows winzip or unix gunzip
Transfer_Size: 877
Digital_Transfer_Option:
Online_Option:
Computer_Contact_Information: Access_Instructions:
The first link will begin a direct download of the data. The second link is a landing page on which all of the downloadable data for a particular region are listed. The third link is a landing page for the entire data catalog.
Fees: none
Technical_Prerequisites:
The downloadable data file has been compressed with the "zip" command and can be unzipped with Winzip (or other tool) on Windows systems. To utilize these data, the user must have software capable of uncompressing the WinZip file and importing and viewing an Esri ArcMap TIFF. Users should download the ArcGIS Project File, SantaBarbaraChannelGIS.mxd.zip, a compressed (with the "zip" command) version of the ArcMap document (.mxd) that has all the data layers loaded in the table of contents for the Santa Barbara Channel region, and has all the data symbolized as on the map sheets. Download and save this ArcGIS project file, including all data layers, to the directory the user has created for this GIS.
Metadata_Reference_Information:
Metadata_Date: 20230501
Metadata_Contact:
Contact_Information:
Contact_Organization_Primary:
Contact_Organization:
U.S. Geological Survey, Pacific Coastal and Marine Science Center
Contact_Person: PCMSC Science Data Coordinator
Contact_Address:
Address_Type: mailing and physical
Address: 2885 Mission Street
City: Santa Cruz
State_or_Province: CA
Postal_Code: 95060-5792
Country: US
Contact_Voice_Telephone: 831-427-4747
Contact_Electronic_Mail_Address: pcmsc_data@usgs.gov
Metadata_Standard_Name: Content Standard for Digital Geospatial Metadata
Metadata_Standard_Version: FGDC-STD-001-1998
Metadata_Time_Convention: local time

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