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Dataset Title:  Coral community structure at Yawazi Point and Tektite in St. John before and
after five hurricanes from 1988\u20132017
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_750060)
Information:  Summary ? | License ? | ISO 19115 | Metadata | Background (external link) | Data Access Form | Files
 
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Things You Can Do With Your Graphs

Well, you can do anything you want with your graphs, of course. But some things you might not have considered are:

The Dataset Attribute Structure (.das) for this Dataset

Attributes {
 s {
  Site {
    String description "Study site";
    String ioos_category "Unknown";
    String long_name "Site";
    String units "unitless";
  }
  Transect_num {
    String description "transect number";
    String ioos_category "Unknown";
    String long_name "Transect Num";
    String units "unitless";
  }
  Year {
    String description "sampling point";
    String ioos_category "Time";
    String long_name "Year";
    String units "years";
  }
  Quadrat {
    Byte _FillValue 127;
    Byte actual_range 1, 30;
    String description "quadrat number. The study was designed to have 10 quadrats along each of 3 lines. Missing quadrats in 1989 represent data lost; each quadrat is ~ 1 x 1 m in size";
    String ioos_category "Unknown";
    String long_name "Quadrat";
    String units "unitless";
  }
  Timing {
    String description "Timing inidcating before and after three episodes of major hurricanes";
    String ioos_category "Unknown";
    String long_name "Timing";
    String units "unitless";
  }
  Orbicella_complex {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 77.0;
    String description "summation of O. annularis O. franksi and O. faveolata";
    String ioos_category "Unknown";
    String long_name "Orbicella Complex";
    String units "percent cover";
  }
  Montastraea {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 7.7;
    String description "M. cavernosa percent cover";
    String ioos_category "Unknown";
    String long_name "Montastraea";
    String units "percent cover";
  }
  Agaricia {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 12.5;
    String description "Agaricia percent cover";
    String ioos_category "Unknown";
    String long_name "Agaricia";
    String units "percent cover";
  }
  Colpophyllia {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 19.9;
    String description "Colpophyllia percent cover";
    String ioos_category "Unknown";
    String long_name "Colpophyllia";
    String units "percent cover";
  }
  Diploria {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 13.1;
    String description "all species in this genus - historic data do not reflect splitting of the genus between Diploria and Pseudodiploria percent cover";
    String ioos_category "Unknown";
    String long_name "Diploria";
    String units "percent cover";
  }
  Eusmilia {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 1.6;
    String description "Eusmilia percent cover";
    String ioos_category "Unknown";
    String long_name "Eusmilia";
    String units "percent cover";
  }
  Madracis {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 1.5;
    String description "Madracis percent cover";
    String ioos_category "Unknown";
    String long_name "Madracis";
    String units "percent cover";
  }
  Meandrina {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 1.5;
    String description "Meandrina percent cover";
    String ioos_category "Unknown";
    String long_name "Meandrina";
    String units "percent cover";
  }
  Porites {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 10.9;
    String description "Porites percent cover";
    String ioos_category "Unknown";
    String long_name "Porites";
    String units "percent cover";
  }
  Siderastrea {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 14.5;
    String description "Siderastrea percent cover";
    String ioos_category "Unknown";
    String long_name "Siderastrea";
    String units "percent cover";
  }
  Mycetophyllia {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 4.0;
    String description "Mycetophyllia percent cover";
    String ioos_category "Unknown";
    String long_name "Mycetophyllia";
    String units "percent cover";
  }
  Acropora {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 6.0;
    String description "Acropora percent cover";
    String ioos_category "Unknown";
    String long_name "Acropora";
    String units "percent cover";
  }
  CTB {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 69.0;
    String description "combined category of crustose coralline algae; algal turf; and bare space percent cover";
    String ioos_category "Unknown";
    String long_name "CTB";
    String units "percent cover";
  }
  Macroalgae {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 75.6;
    String description "summation of macroalgae mostly in the genera Halimeda; Lobophora; Dictyota percent cover";
    String ioos_category "Unknown";
    String long_name "Macroalgae";
    String units "percent cover";
  }
  Coral {
    Float32 _FillValue NaN;
    Float32 actual_range 0.0, 76.3;
    String description "combined coral cover";
    String ioos_category "Unknown";
    String long_name "Coral";
    String units "percent cover";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"Photoquadrats at Yawzi Point and Tektite were recorded using cameras attached
to a framer that held them perpendicular to the reef. A Nikonos V (35-mm
format) was used from 1987-1999, and digital cameras thereafter, with 3.3 MP
resolution from 2000\\u20132006, 6.1 MP from 2006\\u20132010, 12.1 MP in 2011,
16.2 from 2012\\u20132015, and 36.3 MP from 2016\\u2013present. Cameras were
fitted with a strobe (Nikonos SB 105) and the images resolved objects \\u2265
1-cm diameter.
 
The analyses at Yawzi Point and Tektite were augmented in 1992 with six
additional sites that were selected using random coordinates constrained to
hard substrata. This sampling focused on a habitat where boulders and cliffs
of igneous rock are common, mean coral cover has remained < 5%,
and\\u00a0Orbicella annularis\\u00a0has not been common since at least 1992.
Five sites are at 9-m depth, with one at 7-m depth (RS9), and they have been
recorded annually. These sites serve as replicates of reefs between Cabritte
Horn and White Point, and are analyzed as the pooled random sites (PRS).
Results from 1995 (May) and 1996 (May) are used to evaluate the effects of
Hurricanes Luis and Marilyn, and from 2017 (July and November) to evaluate the
effects of Hurricanes Irma and Maria. Each site consists of a permanently
marked transect at a constant depth that was 20-m long from 1992\\u20131999 (n
~ 18 photoquadrats site-1), but was extended to 40 m in 2000 when digital
photography was implemented (n ~ 40 photoquadrats site-1). Photoquadrats (0.5
\\u00d7 0.5 m) were recorded at random positions along each transect (and re-
randomized annually) using cameras (as described above) attached to a framer
that held them perpendicular to the reef. Cameras were attached to two strobes
(Nikonos SB 105), and resolved objects to at least 5-mm diameter.
 
Photoquadrats were analyzed by overlaying them with a grid of 200 randomly-
located dots and identifying the substratum beneath each dot. Images were
analyzed manually prior to 2005, from 2005\\u20132011 using CPCe software, and
from 2012 to present, using CoralNet software with manual annotations. With
this approach, the abundance of each substratum type is defined by the total
number of dots that occur on top of it in each image, and when expressed as a
percentage of the dot population on each image, provides a measure of
percentage cover (hereafter \\u201ccover\\u201d) (Menge 1976). Two resolutions
were applied to the analyses, first to resolve three functional groups (FG),
coral (combined cover of scleractinians), macroalgae (algae \\u2265 1-cm high,
mostly\\u00a0Halimeda, Lobophora, Padina, and\\u00a0Dictyota), and a combined
category of crustose coralline algae, algal turf, and bare space (CTB).
Second, scleractinians were resolved to the lowest taxonomic level possible,
which was genera at Yawzi Point and Tektite, and a combination of species and
genera at the PRS.
 
In addition to the hurricanes described herein, St. John also was impacted by
Hurricane Lenny on 17 November 1999 (Table S1). However, underwater damage
attributed to this storm was minor, probably due to the modest local wind
speeds (150 km h-1), and propagation of damaging waves east and south that
reduced their impacts on the southern shore of St. John. The effects of
Hurricane Lenny are not considered in the present analysis. Given the vagaries
of fieldwork extending over 31 Years, it was not possible to standardize the
timing of sampling that took place before and after each storm episode.
Sampling took place 6 weeks after Hurricane Hugo, 8 months after Hurricane
Luis, and 9 weeks after Hurricane Maria. Sampling after the two most recent
storms was comparable to sampling after Hurricane Hugo with regards to the
delay following the storms and, therefore, probably quantified mostly coral
mortality directly attributable to physical damage, and blooms of macroalgae
commensurate with the growth that is possible in two autumn months. The longer
delay in sampling after Hurricanes Marilyn and Luis probably resulted in
measurements of coral mortality that was caused both by direct physical damage
and delayed-onset disease, as well as blooms of macroalgae that can grow over
8 months extending from autumn to spring.";
    String awards_0_award_nid "55191";
    String awards_0_award_number "DEB-0841441";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0841441&HistoricalAwards=false";
    String awards_0_funder_name "National Science Foundation";
    String awards_0_funding_acronym "NSF";
    String awards_0_funding_source_nid "350";
    String awards_0_program_manager "Saran Twombly";
    String awards_0_program_manager_nid "51702";
    String awards_1_award_nid "55194";
    String awards_1_award_number "DEB-0343570";
    String awards_1_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=0343570&HistoricalAwards=false";
    String awards_1_funder_name "National Science Foundation";
    String awards_1_funding_acronym "NSF";
    String awards_1_funding_source_nid "350";
    String awards_1_program_manager "Saran Twombly";
    String awards_1_program_manager_nid "51702";
    String awards_2_award_nid "562593";
    String awards_2_award_number "DEB-1350146";
    String awards_2_data_url "http://www.nsf.gov/awardsearch/showAward?AWD_ID=1350146";
    String awards_2_funder_name "NSF Division of Environmental Biology";
    String awards_2_funding_acronym "NSF DEB";
    String awards_2_funding_source_nid "550432";
    String awards_2_program_manager "Betsy Von Holle";
    String awards_2_program_manager_nid "701685";
    String awards_3_award_nid "722162";
    String awards_3_award_number "OCE-1801335";
    String awards_3_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1801335";
    String awards_3_funder_name "NSF Division of Ocean Sciences";
    String awards_3_funding_acronym "NSF OCE";
    String awards_3_funding_source_nid "355";
    String awards_3_program_manager "Daniel Thornhill";
    String awards_3_program_manager_nid "722161";
    String cdm_data_type "Other";
    String comment 
"Coral community structure at Yawazi Point and Tektite in St. John before and after five hurricanes from 1988-2017 
  PI: Peter J. Edmunds 
  Version: 2018-11-26";
    String Conventions "COARDS, CF-1.6, ACDD-1.3";
    String creator_email "info@bco-dmo.org";
    String creator_name "BCO-DMO";
    String creator_type "institution";
    String creator_url "https://www.bco-dmo.org/";
    String data_source "extract_data_as_tsv.pl v1.0";
    String date_created "2018-11-27T16:34:58Z";
    String date_modified "2018-11-28T16:21:58Z";
    String defaultDataQuery "&time";
    String doi "10.1575/1912/bco-dmo.750060.1";
    String history 
"2019-06-17T08:32:32Z (local files)
2019-06-17T08:32:32Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_750060.das";
    String infoUrl "https://www.bco-dmo.org/dataset/750060";
    String institution "BCO-DMO";
    String instruments_0_acronym "camera";
    String instruments_0_dataset_instrument_description "Photoquadrats at Yawzi Point and Tektite were recorded using cameras attached to a framer that held them perpendicular to the reef.";
    String instruments_0_dataset_instrument_nid "750065";
    String instruments_0_description "All types of photographic equipment including stills, video, film and digital systems.";
    String instruments_0_instrument_external_identifier "https://vocab.nerc.ac.uk/collection/L05/current/311/";
    String instruments_0_instrument_name "Camera";
    String instruments_0_instrument_nid "520";
    String instruments_0_supplied_name "cameras";
    String keywords "acropora, agaricia, bco, bco-dmo, biological, chemical, colpophyllia, complex, coral, ctb, data, dataset, diploria, dmo, erddap, eusmilia, macroalgae, madracis, management, meandrina, montastraea, mycetophyllia, num, oceanography, office, orbicella, Orbicella_complex, porites, preliminary, quadrat, siderastrea, site, time, timing, transect, Transect_num, year";
    String license 
"The data may be used and redistributed for free but is not intended
for legal use, since it may contain inaccuracies. Neither the data
Contributor, ERD, NOAA, nor the United States Government, nor any
of their employees or contractors, makes any warranty, express or
implied, including warranties of merchantability and fitness for a
particular purpose, or assumes any legal liability for the accuracy,
completeness, or usefulness, of this information.";
    String metadata_source "https://www.bco-dmo.org/api/dataset/750060";
    String param_mapping "{'750060': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/750060/parameters";
    String people_0_affiliation "California State University Northridge";
    String people_0_affiliation_acronym "CSU-Northridge";
    String people_0_person_name "Peter J. Edmunds";
    String people_0_person_nid "51536";
    String people_0_role "Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Woods Hole Oceanographic Institution";
    String people_1_affiliation_acronym "WHOI BCO-DMO";
    String people_1_person_name "Mathew Biddle";
    String people_1_person_nid "708682";
    String people_1_role "BCO-DMO Data Manager";
    String people_1_role_type "related";
    String project "RUI-LTREB Renewal: Three decades of coral reef community dynamics in St. John, USVI: 2014-2019";
    String projects_0_acronym "RUI-LTREB";
    String projects_0_description 
"Describing how ecosystems like coral reefs are changing is at the forefront of efforts to evaluate the biological consequences of global climate change and ocean acidification. Coral reefs have become the poster child of these efforts. Amid concern that they could become ecologically extinct within a century, describing what has been lost, what is left, and what is at risk, is of paramount importance. This project exploits an unrivalled legacy of information beginning in 1987 to evaluate the form in which reefs will persist, and the extent to which they will be able to resist further onslaughts of environmental challenges. This long-term project continues a 27-year study of Caribbean coral reefs. The diverse data collected will allow the investigators to determine the roles of local and global disturbances in reef degradation. The data will also reveal the structure and function of reefs in a future with more human disturbances, when corals may no longer dominate tropical reefs.
The broad societal impacts of this project include advancing understanding of an ecosystem that has long been held emblematic of the beauty, diversity, and delicacy of the biological world. Proposed research will expose new generations of undergraduate and graduate students to natural history and the quantitative assessment of the ways in which our planet is changing. This training will lead to a more profound understanding of contemporary ecology at the same time that it promotes excellence in STEM careers and supports technology infrastructure in the United States. Partnerships will be established between universities and high schools to bring university faculty and students in contact with k-12 educators and their students, allow teachers to carry out research in inspiring coral reef locations, and motivate children to pursue STEM careers. Open access to decades of legacy data will stimulate further research and teaching.";
    String projects_0_end_date "2019-04";
    String projects_0_geolocation "USVI";
    String projects_0_name "RUI-LTREB Renewal: Three decades of coral reef community dynamics in St. John, USVI: 2014-2019";
    String projects_0_project_nid "734983";
    String projects_0_project_website "http://coralreefs.csun.edu/";
    String projects_0_start_date "2014-05";
    String publisher_name "Mathew Biddle";
    String publisher_role "BCO-DMO Data Manager(s)";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v29";
    String summary "These files contain data that support an analysis of the effects of two major hurricanes on coral reefs that have been extensively studied for more than three decades. Major tropical storms are destructive phenomena with large effects on the community dynamics of multiple biomes. On coral reefs, their impacts have been described for decades, leading to the expectation that future storms should have effects similar to those recorded in the past. This expectation relies on the assumption that storm intensities will remain unchanged, and the impacted coral reef communities are similar to those of the recent past; neither assumption is correct. These data support a study quantifying the effects of two category five hurricanes on the reefs of St. John, US Virgin Islands, where 31 y of time-series analyses reveal chronic coral mortality, increasing macroalgal abundance, and five major hurricanes that caused acute coral mortality. Contextualized by these trends, the effects of the most recent storms, Hurricanes Irma and Maria (September 2017), on coral cover were modest. While mean absolute coral cover declined 1\\u20134% depending on site, these effects were not statistically discernable. Following decades of increasing abundance of macroalgae, this functional group responded to the  recent hurricanes with large increases in abundance on both absolute and relative scales. Decades of chronic mortality have changed the coral assemblages of St. John to create degraded communities that are resistant to severe storms.";
    String title "Coral community structure at Yawazi Point and Tektite in St. John before and after five hurricanes from 1988\\u20132017";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.0-alpha";
  }
}

 

Using tabledap to Request Data and Graphs from Tabular Datasets

tabledap lets you request a data subset, a graph, or a map from a tabular dataset (for example, buoy data), via a specially formed URL. tabledap uses the OPeNDAP (external link) Data Access Protocol (DAP) (external link) and its selection constraints (external link).

The URL specifies what you want: the dataset, a description of the graph or the subset of the data, and the file type for the response.

Tabledap request URLs must be in the form
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/datasetID.fileType{?query}
For example,
https://coastwatch.pfeg.noaa.gov/erddap/tabledap/pmelTaoDySst.htmlTable?longitude,latitude,time,station,wmo_platform_code,T_25&time>=2015-05-23T12:00:00Z&time<=2015-05-31T12:00:00Z
Thus, the query is often a comma-separated list of desired variable names, followed by a collection of constraints (e.g., variable<value), each preceded by '&' (which is interpreted as "AND").

For details, see the tabledap Documentation.


 
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