Lisa M. Krigsman
Mary M. Yoklavich
Guy R. Cochrane
Nadine E. Golden
2013
Cup Corals--Santa Barbara Channel, California
Version 1.0, 2012
GeoTIFF
Lisa M. Krigsman
Mary M. Yoklavich
Guy R. Cochrane
Nadine E. Golden
2013
California State Waters Map Series Data Catalog
database
Data Series
DS 781
Reston, VA
U.S. Geological Survey
https://pubs.usgs.gov/ds/781/
Samuel Y. Johnson
Peter Dartnell
Guy R. Cochrane
Nadine E. Golden
Eleyne L. Phillips
Andrew C. Ritchie
Rikk G. Kvitek
H. Gary Greene
Lisa M. Krigsman
Charles A. Endris
Kevin B. Clahan
Ray W. Sliter
Florence L. Wong
Mary M. Yoklavich
William R. Normark
2013
California State Waters Map Series--Hueneme Canyon and vicinity, California
map
Scientific Investigations Map
SIM 3225
Reston, VA
U.S. Geological Survey
https://pubs.usgs.gov/sim/3225/
This part of DS 781 presents data for the map showing the predicted distribution of cup corals in the Santa Barbara Channel, California, region. The raster data file is included in "CupCorals_SantaBarbaraChannel.zip," which is accessible from https://pubs.usgs.gov/ds/781/SantaBarbaraChannel/data_catalog_SantaBarbaraChannel.html.
This map showing the predicted distribution of cup corals in the Santa Barbara Channel is published in Scientific Investigations Map 3225, "California State Waters Map Series--Hueneme Canyon and Vicinity, California" (see sheet 12). In addition, this predicted distribution map will be published in four future California State Waters Map Series SIMs of the region (namely, the Offshore of Ventura, Offshore of Santa Barbara, Offshore of Coal Oil Point, and Offshore of Refugio Beach map areas) [note that, at the time of this writing, one of the other four SIMs has been published: the Offshore of Ventura map area (SIM 3254)].
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 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 the 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 data
presented in sheet 2 (shaded-relief bathymetry), sheet 5 (seafloor-character map), and sheet 6 (ground-truth studies)
of the five SIM publications of the Santa Barbara Channel region that are part of the California State Waters Map Series.
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.
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.
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 ArcInfo format, this metadata file may include some
ArcInfo-specific terminology.
2005
2009
ground condition
As needed
-119.643628
-119.471725
34.390598
34.320467
Global Change Master Directory (GCMD)
Earth Science > Biosphere > Aquatic Ecosystems > Marine Habitat
ISO 19115 Topic Category
biota
oceans
General
biological prediction
fisheries
ecosystem
U.S. Geological Survey
USGS
Coastal and Marine Geology Program
CMGP
Geographic Names Information System (GNIS)
Pacific Ocean
California
Santa Barbara Channel
Hueneme Canyon
Ventura
Santa Barbara
Coal Oil Point
Refugio Beach
None
This information is not intended for navigational purposes.
Read and fully comprehend the metadata prior to data use. Uses of these
data should not violate the spatial resolution of the data. Where
these data are used in combination with other data of different resolution, the resolution of the combined output will be limited by the lowest resolution of all the data.
Acknowledge the U.S. Geological Survey in products derived from these data. Share data products developed using these data with the U.S. Geological Survey.
This database has been approved for release and publication by the Director of the USGS. Although this database has been subjected to rigorous review and is substantially complete, the USGS reserves the right to revise the data pursuant to further analysis and review. Furthermore, it is released on condition that neither the USGS nor the United States Government may be held liable for any damages resulting from its authorized or unauthorized use.
Although this Federal Geographic Data Committee-compliant metadata file is intended to document these data in nonproprietary form, as well as in ArcInfo format, this metadata file may include some ArcInfo-specific terminology.
Lisa M. Krigsman
NOAA National Marine Fisheries Service, Southwest Fisheries Science Center
Biologist
mailing and physical address
NOAA National Marine Fisheries Service, Southwest Fisheries Science Center
Santa Cruz
CA
95060
USA
(831) 420-3971
(831) 420-3977
lisa.krigsman@noaa.gov
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.
Microsoft Windows XP Version 5.1 (Build 2600) Service Pack 3
ESRI ArcCatalog 9.3.1.3500
Pixel resolution 2 m.
Logical Consistency untested.
Please see SIM pamphlet, chapter 5, for
information about omissions, selection criteria, generalization,
definitions used, and other rules used to derive the data set.
On the order of 10 meters.
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. Model inputs.
>
> Cup coral
> taxa~Depth+Class+Block+Class:I(Depth^2)
> # Depth + Class + Block +Class:I(Depth^2) tryCatch(taxa36.glm <- glm(taxa~Depth+Class+Block+Class:I(Depth^2),
> family=binomial(link="logit"), data=taxa.df),
> warning = function(x) { output.df[36,"flag"] <<- 1 },
> finally = taxa36.glm <-
> glm(taxa~Depth+Class+Block+Class:I(Depth^2),
> family=binomial(link="logit"), data=taxa.df)
> )
> summary(taxa36.glm)
>
> MODEL SUMMARY:
> ==============
>
> Call:
> glm(formula = cup_coral ~ Depth + factor(Class) + factor(Block) + factor(Class):I(Depth^2), family = binomial(link="logit"), data = na.omit(d))
>
> Deviance Residuals:
> Min 1Q Median 3Q Max
> -2.36330 -0.52518 -0.19787 -0.05944 3.01412
>
> Coefficients:
> Estimate Std. Error z value Pr(>|z|)
> (Intercept) -5.9189217 1.0497440 -5.638 1.72e-08 ***
> Depth 0.0906923 0.0290678 3.120 0.00181 **
> factor(Class)2 5.0554976 0.6663985 7.586 3.29e-14 ***
> factor(Class)3 6.7506467 0.9527576 7.085 1.39e-12 ***
> factor(Block)2 -0.8342323 0.2385245 -3.497 0.00047 ***
> factor(Block)3 -1.7776564 0.7832775 -2.270 0.02324 *
> factor(Class)1:I(Depth^2) -0.0003605 0.0002207 -1.633 0.10241
> factor(Class)2:I(Depth^2) -0.0006365 0.0002346 -2.713 0.00666 **
> factor(Class)3:I(Depth^2) -0.0008648 0.0003448 -2.508 0.01214 *
> ---
> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
>
> (Dispersion parameter for binomial family taken to be 1)
>
> Null deviance: 992.38 on 922 degrees of freedom
> Residual deviance: 543.69 on 914 degrees of freedom
> AIC: 561.69
>
> Number of Fisher Scoring iterations: 7
>
> Analysis of Deviance Table
>
> Model: binomial, link: logit
>
> Response: cup_coral
>
> Terms added sequentially (first to last)
>
>
> Df Deviance Resid. Df Resid. Dev
> NULL 922 992.38
> Depth 1 123.20 921 869.18
> factor(Class) 2 290.73 919 578.45
> factor(Block) 2 20.96 917 557.49
> factor(Class):I(Depth^2) 3 13.80 914 543.69
>
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.
2010
Raster
Pixel
23905
47950
1
WGS 1984 UTM Zone 11N
0.9996
-117.0
0.0
500000.0
0.0
coordinate pair
0.000000002220024164500956
0.000000002220024164500956
Meter
D WGS 1984
WGS 1984
6378137.0
298.257223563
cupcorals
The raster attributes include VALUE - code for the Predicted-Distribution of Cup Corals for Santa Barbara Channel
Region and COUNT - number of pixels.
ESRI
Rowid
Internal feature number.
ESRI
Sequential unique whole numbers that are automatically generated.
VALUE
VALUE - code for the Predicted-Distribution of Cup Corals for Santa Barbara Channel
Region
USGS
2.22045e-016
.705603
COUNT
The number of pixels (2 m x 2 m size grid cell) represented in each probability raster (see Attribute: VALUE).
ESRI
Sequential unique whole numbers that are automatically generated.
2013
NOAA National Marine Fisheries Service, Southwest Fisheries Science Center
Lisa M. Krigsman
Biologist
mailing and physical address
NOAA National Marine Fisheries Service, Southwest Fisheries Science Center
Santa Cruz
CA
95060
USA
(831) 420-3971
(831) 420-3977
lisa.krigsman@noaa.gov
FGDC Content Standards for Digital Geospatial Metadata
FGDC-STD-001-1998