http://lod.bco-dmo.org/id/dataset/860397
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2021-09-09
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Organized and quality-controlled CalCOFI data for CTD casts and bottle measurements from CalCOFI stations between La Jolla, California to Point Conception between 1984-2019
2021-09-24
publication
2021-09-24
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2022-01-24
publication
https://doi.org/10.26008/1912/bco-dmo.860397.1
Lisa A. Levin
University of California-San Diego Scripps
principalInvestigator
Nicholas Oesch
University of California-San Diego
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: McCormick, L. R., Oesch, N., Levin, L. A. (2022) Organized and quality-controlled CalCOFI data for CTD casts and bottle measurements from CalCOFI stations between La Jolla, California to Point Conception between 1984-2019. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-09-24 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.860397.1 [access date]
Luminoxyscape environmental Dataset Description: Methods and Sampling: <p>This dataset is a subset of data collected by the California Cooperative Oceanic Fisheries Investigations (CalCOFI) long-term monitoring system. All information regarding the sampling program can be found on <a href="https://calcofi.org/about/" target="_blank">https://calcofi.org/about/</a>. Briefly, CalCOFI and the Southern California Coastal Ocean Observing System (SCCOOS) samples a random array within a gridded station map during quarterly cruises and conducts vertical hydrographic casts to ~500-meters (m) depth (or 10 m above bottom where bottom depth &lt; 500 m). More information can be found at: <a href="https://calcofi.org/index.php" target="_blank">https://calcofi.org/index.php</a>. All data used can be found in their original form at:&nbsp;<a href="https://calcofi.org/data/oceanographic-data/ctd-cast-files/" target="_blank">https://calcofi.org/data/oceanographic-data/ctd-cast-files/</a>.</p>
<p>In this analysis, we used data from CalCOFI stations restricted to an area from La Jolla, California to Point Conception (Line 80.0- Line 93.3; 32.95-34.46 °N at shoreline) and 215 kilometers maximum offshore (Station 60; 119.57-121.150 °W). We analyzed daytime casts (09:00-16:00) of both discrete bottle data and continuous CTD casts. This dataset has combined bottle and CTD casts to represent the date range 1984-2019. We used the oxygen and irradiance measurements to determine the visual luminoxyscape for each of the larval species. This range was bounded by the oxygen (partial pressure) where the pO2 would permit 50% minimum retinal function (V50; 13, 7.2, 10.2, and 6.8 kPa for larvae of&nbsp;<em>Doryteuthis opalescens, Octopus bimaculatus, Metacarcinus gracilis, and Pleuroncodes planipes</em>, respectively), and where there is sufficient irradiance for a visual response (0.0311 µmol photons m-2 s-1) for each species.</p>
<p>The "limits" are calculating depths where those oxygen and irradiance requirements would no longer be met. This would be the "visual luminoxyscape depth" (VLD); these depths are presented in the metadata file, “Metadata.Max.Depth.csv.” The limits used to calculate the VLD are “Do.50”, “Ob.50”, “Mg.50”, etc. Oxygen limits for visual physiology were taken from McCormick et al., 2019 (see below for reference).</p>
<p>Additionally, oxygen limits for metabolism were used to determine the depth of occurrence of the Pcrit (the oxygen below which the animal cannot maintain a constant metabolic rate). This was calculated in McCormick, 2019. The depths of occurrence for metabolic limits were determined for larvae of <em>D. opalescens</em> and <em>O. bimaculatus</em>. The dataset columns associated with this are “Do.met” and “Ob.met”.<br />
<br />
<strong>Instruments:</strong><br />
Full details of the instrumentation on the CalCOFI CTD can be found here: <a href="https://calcofi.org/sampling-info/methods/bottle-sampling-methods/" target="_blank">https://calcofi.org/sampling-info/methods/bottle-sampling-methods/</a>.&nbsp;Wherever possible, we used the cruise-corrected data in the "final" cast files provided by CalCOFI, indicating the files already QC by CalCOFI data managers.</p>
<p><strong>Code:</strong><br />
There are 3 R files associated with this dataset: Luminox_May21_Part1_ann.R, Luminox_May21_Part2_ann.R, and Luminox_May21_Part3_ann.R. These are further described in the attached file "<a href="https://datadocs.bco-dmo.org/docs/305/Vision_under_hypoxia/data_docs/Luminoxyscape_Code_Description_of_Files.txt" target="_blank">Luminoxyscape_Code_Description_of_Files.txt</a>". In general:<br />
The code (separated into 3 parts for simplicity and organization) is the entire code dataset from the Luminoxyscape project. The code covers everything including the quality-control for data downloaded directly from CalCOFI (<a href="https://calcofi.org/data/oceanographic-data/ctd-cast-files/" target="_blank">https://calcofi.org/data/oceanographic-data/ctd-cast-files/</a>) in Part 1, the analysis of maximum depths in Part 2 (associated with data "Luminoxyscape maximum depth", and the final analysis for the paper (McCormick et al., Limnology and Oceanography Letters, accepted) including code for all statistics in the analysis and graphs used in the figures. The code is clean and works, but is designed to show the process of the analysis for the project, rather than direct reproducibility. Contact information is included for those who wish to ask questions. All code was run using R (v3.6.3) run through RStudio (v. 2021.09.0).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1829623 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1829623
completed
Lisa A. Levin
University of California-San Diego Scripps
858-534-3579
9500 Gilman Drive Mail Code: 0218
La Jolla
CA
92093-0218
USA
llevin@ucsd.edu
pointOfContact
Nicholas Oesch
University of California-San Diego
858-534-2991
9500 Gilman Dr.
La Jolla
CA
92093-0109
USA
noesch@mail.ucsd.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cast_ID
Line
Station
ISO_DateTime_UTC
dt_PST
Hour
Month
Year
Depth
Temperature
Salinity
SigTheta
PAR
PARCorr
Comb
Latitude
Longitude
O2_mL_L
O2_uM
O2_matm
O2_kPa
Season
Dist_land
Light_Lim
Do_50
Ob_50
Cg_50
Pp_50
Do_met
Ob_met
Loc
ONI
ENSO_Cat
PAR irrandiance sensor QSP-200L
PAR irrandiance sensor QSP-2300
theme
None, User defined
cast
grid_line
station
ISO_DateTime_UTC
Date and time
hour_local
month_local
year
depth
water temperature at measurement depth
salinity from CTD
sigma-theta
PAR
station id
latitude
longitude
dissolved Oxygen
season
track length
irradiance
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
CTD Sea-Bird SBE 911plus
Photosynthetically Available Radiation Sensor
Photosynthetically Available Radiation Sensor
Sea-Bird SBE 13 Dissolved Oxygen Sensor
Sea-Bird SBE 43 Dissolved Oxygen Sensor
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Vision-mediated influence of low oxygen on the physiology and ecology of marine larvae
https://osprey.bco-dmo.org/project/775843
Vision-mediated influence of low oxygen on the physiology and ecology of marine larvae
<p>NSF abstract:<br />
Oxygen is being lost in the ocean worldwide as a result of ocean warming and the input of nutrients from land. Vision requires a large amount of oxygen, and may be less effective or require more light when oxygen is in short supply. This is especially true for active marine animals with complex eyes and visual capabilities, including active arthropods (crabs), cephalopods (squid), and fish. The California coastal waters exhibit a sharp drop in oxygen and light with increasing water depth. This project examines how visual physiology and ecology in young (larval) highly visual marine animals respond to oxygen loss, with a focus on key fisheries and aquaculture species. Experiments and observations will test the hypothesis that oxygen stress will change the light required for these organisms to see effectively, influencing the water depths where they can live and survive. The project will provide interdisciplinary experiences to students and an early career scientist and inform both the public (through outreach at the Birch Aquarium at Scripps Institution of Oceanography) and policy makers about the effects of oxygen decline in the ocean.</p>
<p>Negative effects of oxygen loss on vision have been described for humans and other terrestrial organisms, but never in the marine environment, despite the large changes in oxygen that can occur with depth and over time in the ocean, and the high metabolic demand of visual systems. This project will test the effects of low oxygen on vision in 3 combinations of eye design and photo-transduction mechanisms: compound eye with rhabdomeric photoreceptors (arthropods), simple eye with rhabdomeric photoreceptors (cephalopods), and simple eye with ciliary photoreceptors (fish). A series of oxygen- and light-controlled laboratory experiments will be conducted on representative taxa of each group including the tuna crab, Pleuroncodes planipes; the market squid, Doryteuthis opalescens, and the white sea bass, Atractoscion nobilis. In vivo electrophysiology and behavioral phototaxis experiments will identify new oxygen metrics for visual physiology and function, and will be compared to metabolic thresholds determined in respiration experiments. Hydrographic data collected over 3 decades by the CalCOFI program in the Southern California Bight will be evaluated with respect to visual and metabolic limits to determine the consequences of oxygen variation on the critical luminoxyscape (range of oxygen and light conditions required for visual physiology and function in target species) boundary in each species. Findings for the three vision-based functional groups may test whether oxygen-limited visual responses offer an additional explanation for the shoaling of species distributions among highly visual pelagic taxa in low oxygen, and will help to focus future research efforts and better understand the stressors contributing to habitat compression with expanding oxygen loss in the ocean.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
Vision under hypoxia
largerWorkCitation
project
eng; USA
oceans
-120.823333
-117.27357
31.99666
34.47273
1984-01-05
2019-11-15
Southern California Bight, Northeast Pacific Ocean
0
BCO-DMO catalogue of parameters from Organized and quality-controlled CalCOFI data for CTD casts and bottle measurements from CalCOFI stations between La Jolla, California to Point Conception between 1984-2019
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/860586.rdf
Name: Cast_ID
Units: unitless
Description: <p>Unique cast identification given for each individual hydrographic cast performed by CalCOFI. Character string.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860587.rdf
Name: Line
Units: unitless
Description: <p>CalCOFI sampling grid lines are north/south on a latitudinal grid. See CalCOFI website for details and map. Numeric format.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860588.rdf
Name: Station
Units: unitless
Description: <p>Station. CalCOFI sampling grid stations are east/west on a longitudinal grid. See CalCOFI website for details and map. Numeric format.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860589.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Date/time (in UTC) in ISO8601 format: YYYY-MM-DDThh:mm:ssZ</p>
http://lod.bco-dmo.org/id/dataset-parameter/860590.rdf
Name: dt_PST
Units: unitless
Description: <p>Date/time in Pacific Standard Time (PST). Format: YYYY-MM-DD hh:mm:ss</p>
http://lod.bco-dmo.org/id/dataset-parameter/860591.rdf
Name: Hour
Units: unitless
Description: <p>Hour of the day in PST. Format is numeric 1-23.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860592.rdf
Name: Month
Units: unitless
Description: <p>Month of the year. Numeric, 1-12.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860593.rdf
Name: Year
Units: unitless
Description: <p>Year of the data. Numeric.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860594.rdf
Name: Depth
Units: meters
Description: <p>Depth of data (CTD cast or bottle measurement) Numeric.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860595.rdf
Name: Temperature
Units: degrees Celsius
Description: <p>Temperature. Numeric.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860596.rdf
Name: Salinity
Units: PSU
Description: <p>Salinity in PSU. Numeric.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860597.rdf
Name: SigTheta
Units: 1000 kg m-3
Description: <p>Sigma theta is the density of seawater calculated with in situ salinity, potential temperature, and pressure =0 minus 1000 kg m-3.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860598.rdf
Name: PAR
Units: µmol photons m-2 s-1
Description: <p>Photosynthetically Active Radiation. A measure of irradiance between ~400-700 nm.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860599.rdf
Name: PARCorr
Units: µmol photons m-2 s-1
Description: <p>PAR weighted to the animal’s spectral sensitivity. In this case, all PAR was multiplied by 0.34, as the percentage of PAR each species could detect. See McCormick et al., 2019 for additional details.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860600.rdf
Name: Comb
Units: unitless
Description: <p>A combined Line/Station code used for sorting data.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860601.rdf
Name: Latitude
Units: decimal degrees North
Description: <p>Latitude of the cast. Numeric format.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860602.rdf
Name: Longitude
Units: decimal degrees East
Description: <p>Longitude of the cast. Numeric format.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860603.rdf
Name: O2_mL_L
Units: milliliters per liter
Description: <p>Oxygen concentration. Numeric format.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860604.rdf
Name: O2_uM
Units: µmol photons per kiligram
Description: <p>Oxygen content</p>
http://lod.bco-dmo.org/id/dataset-parameter/860605.rdf
Name: O2_matm
Units: milliatmospheres
Description: <p>Oxygen content. Numeric</p>
http://lod.bco-dmo.org/id/dataset-parameter/860606.rdf
Name: O2_kPa
Units: partial pressure units (kPa)
Description: <p>Oxygen content. Numeric.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860607.rdf
Name: Season
Units: unitless
Description: <p>Season for data. Winter (December, January, February); Spring (March, April, May); Summer (June, July, August); and Fall (September, October, November).</p>
http://lod.bco-dmo.org/id/dataset-parameter/860608.rdf
Name: Dist_land
Units: kilometers
Description: <p>Distance from land, calculated as the spherical distance from the station to the corresponding shore station, or distance from the nearest island, for stations close to the Channel Islands.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860609.rdf
Name: Light_Lim
Units: unitless
Description: <p>Whether the larvae of all 4 species would have sufficient irradiance for >5% visual function at that specific cast depth bin. TRUE: Animals would have irradiance for >5% visual function; FALSE: Animals would have irradiance for <5% visual function. Based on McCormick et al., 2019. Character format (TRUE/FALSE).</p>
http://lod.bco-dmo.org/id/dataset-parameter/860610.rdf
Name: Do_50
Units: unitless
Description: <p>Whether larvae of Doryteuthis opalescens would have oxygen sufficient for >50% visual function at the specific cast depth bin. Character format, TRUE/FALSE. TRUE: Larvae would have oxygen for >50% visual function. FALSE: Larvae would have oxygen for <50% visual function.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860611.rdf
Name: Ob_50
Units: unitless
Description: <p>Whether larvae of Octopus bimaculatus would have oxygen sufficient for >50% visual function at the specific cast depth bin. Character format, TRUE/FALSE. TRUE: Larvae would have oxygen for >50% visual function. FALSE: Larvae would have oxygen for <50% visual function.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860612.rdf
Name: Cg_50
Units: unitless
Description: <p>Whether larvae of Metacarcinus gracilis would have oxygen sufficient for >50% visual function at the specific cast depth bin. Character format, TRUE/FALSE. TRUE: Larvae would have oxygen for >50% visual function. FALSE: Larvae would have oxygen for <50% visual function.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860613.rdf
Name: Pp_50
Units: unitless
Description: <p>Whether larvae of Pleuroncodes planipes would have oxygen sufficient for >50% visual function at the specific cast depth bin. Character format, TRUE/FALSE. TRUE: Larvae would have oxygen for >50% visual function. FALSE: Larvae would have oxygen for <50% visual function.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860614.rdf
Name: Do_met
Units: unitless
Description: <p>Whether larvae of D. opalescens would have oxygen sufficient for maintaining a stable metabolic rate (oxygen > Pcrit) at the specific cast depth bin. Character format, TRUE/FALSE. TRUE: Larvae would have oxygen >Pcrit. FALSE: Larvae would have oxygen for <Pcrit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860615.rdf
Name: Ob_met
Units: unitless
Description: <p>Whether larvae of O. bimaculatus would have oxygen sufficient for maintaining a stable metabolic rate (oxygen > Pcrit) at the specific cast depth bin. Character format, TRUE/FALSE. TRUE: Larvae would have oxygen >Pcrit. FALSE: Larvae would have oxygen for <Pcrit.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860616.rdf
Name: Loc
Units: unitless
Description: <p>Categorical location of the station; whether the station was considered nearshore (“NS”; <30 km from shore) or offshore (“OS”; 30-215 km from shore). Character.</p>
http://lod.bco-dmo.org/id/dataset-parameter/860617.rdf
Name: ONI
Units: unitless
Description: <p>Oceanic Niño Index from the NOAA Climate Prediction Center. The Index measures the temperature anomaly in the 3.4 region in the equatorial Pacific. Numeric; positive values indicate warming, negative values indicate cooling. Data taken from: <a href="https://origin.cpc.ncep.noaa.gov/products/analysis_monitoring/ensostuff/ONI_v5.php" target="_blank">https://origin.cpc.ncep.noaa.gov/products/analysis_monitoring/ensostuff/ONI_v5.php</a></p>
http://lod.bco-dmo.org/id/dataset-parameter/860618.rdf
Name: ENSO_Cat
Units: unitless
Description: <p>Categorical description of El Niño-Southern Oscillation phase. Categories were determined using the ONI. Winter/Spring ONI values of >=1 were considered “El Niño” years, values <= -1 were considered “La Niña” years; all other years were considered “non-ENSO” years.</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
87846808
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/ee337ed1-ec48-5efb-8e62-70287092aa71/content
download
https://doi.org/10.26008/1912/bco-dmo.860397.1
download
onLine
dataset
<p>This dataset is a subset of data collected by the California Cooperative Oceanic Fisheries Investigations (CalCOFI) long-term monitoring system. All information regarding the sampling program can be found on <a href="https://calcofi.org/about/" target="_blank">https://calcofi.org/about/</a>. Briefly, CalCOFI and the Southern California Coastal Ocean Observing System (SCCOOS) samples a random array within a gridded station map during quarterly cruises and conducts vertical hydrographic casts to ~500-meters (m) depth (or 10 m above bottom where bottom depth &lt; 500 m). More information can be found at: <a href="https://calcofi.org/index.php" target="_blank">https://calcofi.org/index.php</a>. All data used can be found in their original form at:&nbsp;<a href="https://calcofi.org/data/oceanographic-data/ctd-cast-files/" target="_blank">https://calcofi.org/data/oceanographic-data/ctd-cast-files/</a>.</p>
<p>In this analysis, we used data from CalCOFI stations restricted to an area from La Jolla, California to Point Conception (Line 80.0- Line 93.3; 32.95-34.46 °N at shoreline) and 215 kilometers maximum offshore (Station 60; 119.57-121.150 °W). We analyzed daytime casts (09:00-16:00) of both discrete bottle data and continuous CTD casts. This dataset has combined bottle and CTD casts to represent the date range 1984-2019. We used the oxygen and irradiance measurements to determine the visual luminoxyscape for each of the larval species. This range was bounded by the oxygen (partial pressure) where the pO2 would permit 50% minimum retinal function (V50; 13, 7.2, 10.2, and 6.8 kPa for larvae of&nbsp;<em>Doryteuthis opalescens, Octopus bimaculatus, Metacarcinus gracilis, and Pleuroncodes planipes</em>, respectively), and where there is sufficient irradiance for a visual response (0.0311 µmol photons m-2 s-1) for each species.</p>
<p>The "limits" are calculating depths where those oxygen and irradiance requirements would no longer be met. This would be the "visual luminoxyscape depth" (VLD); these depths are presented in the metadata file, “Metadata.Max.Depth.csv.” The limits used to calculate the VLD are “Do.50”, “Ob.50”, “Mg.50”, etc. Oxygen limits for visual physiology were taken from McCormick et al., 2019 (see below for reference).</p>
<p>Additionally, oxygen limits for metabolism were used to determine the depth of occurrence of the Pcrit (the oxygen below which the animal cannot maintain a constant metabolic rate). This was calculated in McCormick, 2019. The depths of occurrence for metabolic limits were determined for larvae of <em>D. opalescens</em> and <em>O. bimaculatus</em>. The dataset columns associated with this are “Do.met” and “Ob.met”.<br />
<br />
<strong>Instruments:</strong><br />
Full details of the instrumentation on the CalCOFI CTD can be found here: <a href="https://calcofi.org/sampling-info/methods/bottle-sampling-methods/" target="_blank">https://calcofi.org/sampling-info/methods/bottle-sampling-methods/</a>.&nbsp;Wherever possible, we used the cruise-corrected data in the "final" cast files provided by CalCOFI, indicating the files already QC by CalCOFI data managers.</p>
<p><strong>Code:</strong><br />
There are 3 R files associated with this dataset: Luminox_May21_Part1_ann.R, Luminox_May21_Part2_ann.R, and Luminox_May21_Part3_ann.R. These are further described in the attached file "<a href="https://datadocs.bco-dmo.org/docs/305/Vision_under_hypoxia/data_docs/Luminoxyscape_Code_Description_of_Files.txt" target="_blank">Luminoxyscape_Code_Description_of_Files.txt</a>". In general:<br />
The code (separated into 3 parts for simplicity and organization) is the entire code dataset from the Luminoxyscape project. The code covers everything including the quality-control for data downloaded directly from CalCOFI (<a href="https://calcofi.org/data/oceanographic-data/ctd-cast-files/" target="_blank">https://calcofi.org/data/oceanographic-data/ctd-cast-files/</a>) in Part 1, the analysis of maximum depths in Part 2 (associated with data "Luminoxyscape maximum depth", and the final analysis for the paper (McCormick et al., Limnology and Oceanography Letters, accepted) including code for all statistics in the analysis and graphs used in the figures. The code is clean and works, but is designed to show the process of the analysis for the project, rather than direct reproducibility. Contact information is included for those who wish to ask questions. All code was run using R (v3.6.3) run through RStudio (v. 2021.09.0).</p>
Specified by the Principal Investigator(s)
<p><strong>Data Processing:</strong>Full details on the CTD processing procedure can be found here:&nbsp;<a href="https://calcofi.org/sampling-info/methods/bottle-sampling-methods/" target="_blank">https://calcofi.org/sampling-info/methods/bottle-sampling-methods/</a></p>
<p>Programs used to analyze data include SeaBird SBEDataProcessing version 7.26.7</p>
<p><strong>BCO-DMO Processing:</strong><br />
- Converted dates to ISO8601 date format in a new column;<br />
- Adjusted field/parameter names to comply with BCO-DMO naming conventions;<br />
- Missing data identifier ‘NA’ replaced with 'nd' (BCO-DMO's default missing data identifier);<br />
- Added a conventional header with dataset name, PI names, version date;<br />
- In the ENSO_Cat column, replaced "La Niña" with "La Nina" and "El Niño" with "El Nino".</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
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PI Supplied Instrument Name: PI Supplied Instrument Description:The Sea-Bird SBE 911plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9plus and SBE 11plus is called a SBE 911plus. The SBE 9plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3plus and SBE 4). The SBE 9plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
PAR irrandiance sensor QSP-200L
PAR irrandiance sensor QSP-200L
PI Supplied Instrument Name: PAR irrandiance sensor QSP-200L PI Supplied Instrument Description:PAR irradiance sensor QSP-200L from Biospherical Instruments, Inc. (http://www.biospherical.com/) Instrument Name: Photosynthetically Available Radiation Sensor Instrument Short Name:PAR sensor Instrument Description: A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/122/
PAR irrandiance sensor QSP-2300
PAR irrandiance sensor QSP-2300
PI Supplied Instrument Name: PAR irrandiance sensor QSP-2300 PI Supplied Instrument Description:PAR irradiance sensor QSP-2300 from Biospherical Instruments, Inc. (http://www.biospherical.com/). Instrument Name: Photosynthetically Available Radiation Sensor Instrument Short Name:PAR sensor Instrument Description: A PAR sensor measures photosynthetically available (or active) radiation. The sensor measures photon flux density (photons per second per square meter) within the visible wavelength range (typically 400 to 700 nanometers). PAR gives an indication of the total energy available to plants for photosynthesis. This instrument name is used when specific type, make and model are not known. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/122/
PI Supplied Instrument Name: Instrument Name: Sea-Bird SBE 13 Dissolved Oxygen Sensor Instrument Short Name:SBE-13 DO Instrument Description: Dissolved oxygen sensor with either a Beckmann (SBE 13B) or YSI polarographic element (SBE 13Y limited to 2000m depth). Designed to interface with the SBE 9 and 9plus CTD underwater units. An optional plenum to connect into the pumped plumbing system was available but usage with the membrane exposed was possible. Replaced by the SBE 43 in 2001.
PI Supplied Instrument Name: Instrument Name: Sea-Bird SBE 43 Dissolved Oxygen Sensor Instrument Short Name:SBE-43 DO Instrument Description: The Sea-Bird SBE 43 dissolved oxygen sensor is a redesign of the Clark polarographic membrane type of dissolved oxygen sensors. more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0036/