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Dataset Title:  Names, codes, and characteristics of species observed during reef surveys in
the Bahamas (Lionfish Invasion project)
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Institution:  BCO-DMO   (Dataset ID: bcodmo_dataset_3896)
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 {
  species_code {
    String bcodmo_name "taxon_code";
    String description "4-letter genus species code (typically first two letters are the first two of the genus and last two letters are the first two of the species - corresponds with \"Species\" column in \"LLLE Surveys clean\" dataset). Originally named 'SpeciesID'.";
    String long_name "Species Code";
    String units "dimensionless";
  }
  species {
    String bcodmo_name "species";
    String description "Scientific name of species (Genus species) at the beginning of the project.";
    String long_name "Species";
    String units "text";
  }
  name_change {
    Byte _FillValue 127;
    Byte actual_range 0, 1;
    String bcodmo_name "unknown";
    String description "Indicates whether or not there has been a name change for the species since the inception of the project (0 = no change, 1 = change).";
    String long_name "Name Change";
    String units "0 or 1";
  }
  species_new {
    String bcodmo_name "species";
    String description "Currently recognized scientific name of species (should match \"SpeciesName\" if \"NameChange\" = 0, and should contain the more recent version of the name if \"NameChange\" = 1). Column originally named 'NewName'.";
    String long_name "Species New";
    String units "text";
  }
  common_name {
    String bcodmo_name "common_name";
    String description "Common name of the species.";
    String long_name "Common Name";
    String units "text";
  }
  family {
    String bcodmo_name "family";
    String description "Family of species.";
    String long_name "Family";
    String units "text";
  }
  transient {
    Byte _FillValue 127;
    Byte actual_range 0, 1;
    String bcodmo_name "unknown";
    String description "Takes value of 1 if species is primarily transient at the experimental reef scale and 0 otherwise.";
    String long_name "Transient";
    String units "0 or 1";
  }
  piscivore {
    Byte _FillValue 127;
    Byte actual_range 0, 1;
    String bcodmo_name "unknown";
    String description "Takes value of 1 if species is primarily a piscivore and 0 otherwise.";
    String long_name "Piscivore";
    String units "0 or 1";
  }
  herbivore {
    Byte _FillValue 127;
    Byte actual_range 0, 1;
    String bcodmo_name "unknown";
    String description "Takes value of 1 if species is primarily an herbivore and 0 otherwise.";
    String long_name "Herbivore";
    String units "0 or 1";
  }
  mature_lt_5cm {
    Byte _FillValue 127;
    Byte actual_range 0, 1;
    String bcodmo_name "unknown";
    String description "Takes value of 1 if species reaches reproductive maturity at a TL of less than or equal to 5 cm and 0 otherwise. Originally named 'MatLess5'.";
    String long_name "Mature Lt 5cm";
    String units "0 or 1";
  }
  obligate_cleaner {
    Byte _FillValue 127;
    Byte actual_range 0, 1;
    String bcodmo_name "unknown";
    String description "Takes value of 1 if species is documented as an obligate cleaner and 0 otherwise.";
    String long_name "Obligate Cleaner";
    String units "0 or 1";
  }
  faculative_cleaner {
    Byte _FillValue 127;
    Byte actual_range 0, 1;
    String bcodmo_name "unknown";
    String description "Takes value of 1 if species is documented as a faculative cleaner and 0 otherwise.";
    String long_name "Faculative Cleaner";
    String units "0 or 1";
  }
  invertebrate {
    Byte _FillValue 127;
    Byte actual_range 0, 1;
    String bcodmo_name "unknown";
    String description "Takes value of 1 if species is an invertebrate and 0 if species is a fish.";
    String long_name "Invertebrate";
    String units "0 or 1";
  }
  LW_a {
    Float32 _FillValue NaN;
    Float32 actual_range 1.0e-5, 1.22482;
    String bcodmo_name "unknown";
    String description "Parameter \"a\" in corrected length-weight conversion equation used for biomass calculations.";
    String long_name "LW A";
    String units "numeric";
  }
  LW_b {
    Float32 _FillValue NaN;
    Float32 actual_range 1.75112, 3.84677;
    String bcodmo_name "unknown";
    String description "Parameter \"b\" in corrected length-weight conversion equation used for biomass calculations.";
    String long_name "LW B";
    String units "numeric";
  }
  LW_c {
    Float32 _FillValue NaN;
    Float32 actual_range 0.7704, 10.0;
    String bcodmo_name "unknown";
    String description "Standard length to total length conversion parameter (LWc = 1 if \"a\" and \"b\" were fit on total length and LWc equals ratio of SL to TL if \"a\" and \"b\" were fit on standard length.";
    String long_name "LW C";
    String units "numeric";
  }
  LW_ref {
    Byte _FillValue 127;
    Byte actual_range 2, 16;
    String bcodmo_name "unknown";
    String description "Reference code identifying source of LW conversion parameters.";
    String long_name "LW Ref";
    String units "code";
  }
  species_substitute {
    String bcodmo_name "species";
    String description "Name of substitute species used for LW conversion parameters (if parameters could not be found for a given species those for a similarly shaped species were used - SubSp is equal to \"na\" if parameters for the actual species were used).";
    String long_name "Species Substitute";
    String units "text";
  }
 }
  NC_GLOBAL {
    String access_formats ".htmlTable,.csv,.json,.mat,.nc,.tsv";
    String acquisition_description 
"This long-term, large-scale field experiment was designed to document the
community-wide effects of invasive lionfish in the vicinity of Lee Stocking
Island, Bahamas. Baseline surveys of the fish community were conducted at each
of ten large (1400 to 4000 m2) reefs by counting and sizing all fishes within
two permanent square plots (100 m2) and four permanent strip plots (50 m2) at
each reef. Square plots were centered on the area of each reef with the
greatest three-dimensional structure, whereas strip transects were placed to
provide a representative sample of the entire reef (biased towards hard
substrate). The reefs were paired based on habitat characteristics (depth,
current, predominant substrate type, etc.), and one reef in each pair was
designated as either low-lionfish-density (LLD) or high-lionfish-density
(HLD). Lionfish were then removed from LLD reefs and added to HLD reefs. We
attempted to remove all lionfish from LLD reefs, and to augment the density of
lionfish on HLD reefs to the level observed on the highest-density reefs
before the experiment. Surveys of each fish community were then repeated
approximately quarterly. During each survey, any new lionfish appearing on LLD
reefs were removed and distributed evenly across the HLD reefs (again,
ensuring that densities at HLD reefs did not exceed natural invasive densities
prior to the experiment). See details in the following related publications.
 
Related Publications:  
 Albins, M.A. (2012) Effects of the Invasive Pacific Red Lionfish Pterois
volitans on Native Atlantic Coral-reef Fish Communities (Chapter 6). PhD
Dissertation. Oregon State University, Corvallis, Oregon.  
 Albins, M.A. (in preparation) Invasive Pacific lionfish Pterois volitans
reduce abundance and species richness of native Bahamian coral-reef fishes:
results from a large-scale, long-term experiment. Intended for Ecological
Applications.";
    String awards_0_award_nid "55160";
    String awards_0_award_number "OCE-0851162";
    String awards_0_data_url "http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=0851162";
    String awards_0_funder_name "NSF Division of Ocean Sciences";
    String awards_0_funding_acronym "NSF OCE";
    String awards_0_funding_source_nid "355";
    String awards_0_program_manager "David L. Garrison";
    String awards_0_program_manager_nid "50534";
    String cdm_data_type "Other";
    String comment 
"List of species observed during surveys 
 Lead PI: Mark Hixon (OSU) 
 Sub-Project Lead: Mark A. Albins (OSU) 
 Version: 19 March 2013";
    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 version 2.3  19 Dec 2019";
    String date_created "2013-03-19T18:40:12Z";
    String date_modified "2019-10-28T17:27:14Z";
    String defaultDataQuery "&time<now";
    String doi "10.1575/1912/bco-dmo.3896.1";
    String history 
"2020-08-06T01:16:23Z (local files)
2020-08-06T01:16:23Z https://erddap.bco-dmo.org/tabledap/bcodmo_dataset_3896.das";
    String infoUrl "https://www.bco-dmo.org/dataset/3896";
    String institution "BCO-DMO";
    String keywords "5cm, bco, bco-dmo, biological, change, chemical, cleaner, code, common, common_name, data, dataset, dmo, erddap, faculative, faculative_cleaner, family, herbivore, invertebrate, LW_a, LW_b, LW_c, LW_ref, management, mature, mature_lt_5cm, name, name_change, new, obligate, obligate_cleaner, oceanography, office, piscivore, preliminary, ref, species, species_code, species_new, species_substitute, substitute, transient";
    String license "https://www.bco-dmo.org/dataset/3896/license";
    String metadata_source "https://www.bco-dmo.org/api/dataset/3896";
    String param_mapping "{'3896': {}}";
    String parameter_source "https://www.bco-dmo.org/mapserver/dataset/3896/parameters";
    String people_0_affiliation "Oregon State University";
    String people_0_affiliation_acronym "OSU";
    String people_0_person_name "Mark Hixon";
    String people_0_person_nid "51647";
    String people_0_role "Lead Principal Investigator";
    String people_0_role_type "originator";
    String people_1_affiliation "Oregon State University";
    String people_1_affiliation_acronym "OSU";
    String people_1_person_name "Mark  A Albins";
    String people_1_person_nid "51666";
    String people_1_role "Scientist";
    String people_1_role_type "originator";
    String people_2_affiliation "Woods Hole Oceanographic Institution";
    String people_2_affiliation_acronym "WHOI BCO-DMO";
    String people_2_person_name "Shannon Rauch";
    String people_2_person_nid "51498";
    String people_2_role "BCO-DMO Data Manager";
    String people_2_role_type "related";
    String project "Lionfish Invasion";
    String projects_0_acronym "Lionfish Invasion";
    String projects_0_description 
"Invasive species are increasingly introduced by human activities to new regions of the world where those species have never existed previously. In the absence of natural enemies (predators, competitors, and diseases) from their homeland, invasives may have strong negative effects on invaded ecosystems, especially systems with fewer species (\"ecological release\"), and may even drive native species extinct. However, if native natural enemies can somehow control the invaders (\"ecological resistance\"), then ecological disruption can be prevented or at least moderated. Most of the many invasive species in the sea have been seaweeds and invertebrates, and the few documented invasive marine fishes have not caused major problems. However, this situation has recently changed in a stunning and ominous way. In the early 1990s, lionfish (Pterois volitans) from the Pacific Ocean were accidentally or intentionally released from aquaria to the ocean in the vicinity of Florida. Camouflaged by shape and color, protected by venomous spines, consuming native coral-reef fishes voraciously, and reproducing rapidly, lionfish have subsequently undergone a population explosion. They now range from the mid-Atlantic coast of the US to the Caribbean, including the Bahamas. Native Atlantic fishes have never before encountered this spiny, stealthy, efficient predator and seldom take evasive action. In fact, the investigator has documented that a single lionfish is capable of reducing the abundance of small fish on a small coral patch reef by nearly 80% in just 5 weeks. There is great concern that invasive lionfish may severely reduce the abundance of native coral-reef fishes important as food for humans (e.g., grouper and snapper in their juvenile stages) as well as species that normally maintain the integrity of coral reefs (e.g., grazing parrotfishes that can prevent seaweeds from smothering corals). There are far more species of coral-reef fish in the Pacific than the Atlantic, so this invasion may represent a case of extreme ecological release with minor ecological resistance. Dr. Hixon and colleagues will study the mechanisms of ecological release in lionfish, as well as examine potential sources of ecological resistance in the heavily invaded Bahamas. Because very little is known about the ecology and behavior of lionfish in their native Pacific range, he will also conduct comparative studies in both oceans, which may provide clues regarding the extreme success of this invasion. In the Bahamas, the investigator will document the direct and indirect effects on native species of the ecological release of lionfish, both as a predator and as a competitor. These studies will be conducted at various scales of time and space, from short-term experiments on small patch reefs, to long-term experiments and observations on large reefs. Whereas direct effects involve mostly changes in the abundance of native species, indirect effects can be highly variable. For example, lionfish may actually indirectly benefit some native species by either consuming or outcompeting the competitors of those natives. The project will explore possible ecological resistance to the invasion by determining whether any native Bahamian species are effective natural enemies of lionfish, including predators, parasites, and competitors of both juvenile and adult lionfish. Comparative studies of natural enemies, as well as lionfish ecology and behavior, in both the Atlantic and the Pacific may provide clues regarding the explosive spread of lionfish in the Atlantic.
Regarding broader impacts, this basic research will provide information valuable to coral-reef and fisheries managers fighting the lionfish invasion in the US, the Bahamas, and the greater Caribbean, especially if sources of native ecological resistance are identified. The study will fund the PhD research of U.S. graduate students, as well as involve assistance and participation by a broad variety of undergraduates and reef/fisheries managers, including women, minorities, native Bahamians, and native Pacific islanders. Participation in this project will promote education in marine ecology and conservation biology directly via Dr. Hixon's and graduate students' teaching and outreach activities, and indirectly via the experiences of undergraduate field assistants and various associates.";
    String projects_0_end_date "2012-11";
    String projects_0_geolocation "Bahamas; Cayman Islands; Mariana Islands; Philippines";
    String projects_0_name "Ecological Release and Resistance at Sea: Invasion of Atlantic Coral Reefs by Pacific Lionfish";
    String projects_0_project_nid "2256";
    String projects_0_project_website "http://hixon.science.oregonstate.edu/content/highlight-lionfish-invasion";
    String projects_0_start_date "2009-06";
    String publisher_name "Biological and Chemical Oceanographic Data Management Office (BCO-DMO)";
    String publisher_type "institution";
    String sourceUrl "(local files)";
    String standard_name_vocabulary "CF Standard Name Table v55";
    String summary "Names, codes, and characteristics of species observed during reef surveys in the Bahamas (Lionfish Invasion project).";
    String title "Names, codes, and characteristics of species observed during reef surveys in the Bahamas (Lionfish Invasion project)";
    String version "1";
    String xml_source "osprey2erddap.update_xml() v1.3";
  }
}

 

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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