%
%  Narragansett Bay NERR 

% The preceding empty line is important
% $Log: nbnerr.m,v $
% Revision 1.4  1999/07/21 15:34:00  dbyrne
%
%
% Corrected spelling of 'Dissolved', corrected language in comments.
% -- dbyrne 99/07/21
%
% Revision 1.3  1999/07/15 20:10:20  kwoklin
% Change Oxygen to Dissolved_Oxygen.   klee
%
% Revision 1.1  1999/06/07 16:06:28  paul
% renamed nbneer.m to nbnerr.m     renamed nbneeru.m to nbnerru.m
% renamed nbneeru to nbnerru inside nbnerr.m
%
% Revision 1.2  1999/06/07 15:41:36  paul
% change NEER to NERR
%
% Revision 1.1  1999/06/01 07:10:34  dbyrne
%
%
% Moved up from kleedata/
%
% Revision 1.5  1999/05/28 22:53:06  kwoklin
% Point to new server for all jgofs datasets. Update getjgsta on loaddods.
% Fix infotext for all gb geturl files. Fix transmissivity for some gb
% files. Modify some variable names on gb files.       klee
%

% $Id: nbnerr.m,v 1.4 1999/07/21 15:34:00 dbyrne Exp $
% klee 02/99

GetFunctionName = 'getjgsta';
Server = 'http://maewest.gso.uri.edu/cgi-bin/nph-jg/nbnerr';
CatalogServer = nan;
URL_m_File = 'nbnerru';

IntervalTime = 0.5;  %in hr
LonRange = [-71.40 -71.26];
LatRange = [41.52 41.70];
TimeRange = [1995.92482 1999.00];
DepthRange = [0.0 9.1];
Resolution = nan;

DodsName1 = str2mat('stationno','mintime','maxtime','lat','lon','time');
DodsName = str2mat('temp','sal','do','ph','turb','dop','stationno');
DataName = 'Water Column - Narragansett Bay - URI';       % Name for this dataset.
LongitudeName = 'lon';
LatitudeName = 'lat';
TimeName = 'time';          
DepthName = 'depth';
DepthUnits = 'Meters';
SelectableVariables = str2mat('Sea_Temp','Salinity', ...
    'Dissolved_Oxygen','pH_Value', ...
    'Turbidity','Oxygen_Saturation');
TextField = str2mat('Potters_Cove','T-wharf');
OptionalVariables = str2mat('spcond');
SelectableOptional = str2mat('Spec_Cond');

DataNull=[nan nan nan nan 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0];

Acknowledge = sprintf('%s\n', ...
    [ 'The author of this dataset is A. D. Beck.  ', ...
      'The data were provided by the Graduate School of Oceanography at ',...
      'University of Rhode Island and accessed via ', ...
      'the Distributed Oceanographic Data System (DODS: ', ...
      'http://www.unidata.ucar.edu/packages/dods).']);
Data_Use_Policy = [];

%COMMENTS
Comments1 = sprintf('%s\n',...
'   ',...
'              Narragansett Bay National Estuarine Research Reserve (NB NERR)',...
'   ',...
 '           Parameter         Description                    Units',...
'      --------------------------------------------------------------------------',...
'            time              yearday                        decimal years',...
'            depth             tidal height                   meters',...
'            temp              sea temp                       degrees C',...
'            salinity          salinity                       ppt',...
'            spcond            specific conductivity          mS/cm',...
'            do                dissolved oxygen               ppm',...
'            dop               dissolved oxygen               percent saturation',...
'            ph                pH value                       pH units',...
'            turb              turbidity                      NTU',...
'   ',...
'(Jan - Dec 1998)',...
'Latest update: Dec 28, 1998',...
'   ',...
'I.  Data set and Research Descriptors',...
'   ',...
'1.  Principle investigators and contact persons.',...
'   ',...
'Allan D. Beck, Manager		Susan C. Adamowicz, Research Associate',...
'Narragansett Bay NERR		University of Rhode Island',...
'422 Narragansett Ave.		Graduate School of Oceanography',...
'Prudence Island, RI 02872      South Ferry Road',...
'				Narragansett, RI  02882',...
'Tel: (401) 683-6780		Tel: (401) 874-6617',...
'Fax: (401) 682-1936		Fax: (401) 874-6613',...
'				Email:  scadam@gsosun1.gso.uri.edu',...
'   ',...
'2.  Entry verification.',...
'   ',...
'Other water quality measurements are made by standard field methods at the time of datalogger',...
'deployment and weekly thereafter.  Results are compared with YSI 6000 data records.  Data may ',...
'be corrected based on the comparative analyses and is then so noted in the data anomaly section ',...
'of the metadata form.');

Comments2 = sprintf('%s\n',...
'Temperature is measured by mercury thermometer calibrated with a NBS certified thermometer. ',...
'Dissolved oxygen is determined by a modified Winkler titration.  Salinity is measured with a ',...
'Hydrolab Surveyor 3 equipped with a salinity/ conductivity sensor.  The pH is determined by ',...
'a Corning benchtop pH meter.  Turbidity is presently measured with a Secchi disk.  (This method ',...
'does not provide data that is comparable to the YSI data.  An appropriate method recommended by ',...
'the manufacturer and accepted by the scientific community will be used in the future.) ',...
'Allan Beck is responsible for these water quality measurements.',...
'   ',...
'Data is uploaded to a PC from the YSI datalogger using the PC6000 software in both the PC6000 ',...
'format and in comma delimited format.  The comma-delimited data is opened in Excel 5.0 and edited ',...
'to remove headers and extra spaces.  Each file contains a month''s data and missing days are denoted',...
'by periods.  ',...
'   ',...
'3.  Research objectives.',...
'   ',...
'YSI6000 dataloggers are being deployed off Prudence Island in Narragansett Bay as part of the ',...
'National Estuarine Research Reserve''s (NERR) Water Quality Monitoring Program. The goal is to ',...
'develop long-term data sets for representative estuarine systems in order to track changes in ',...
'water quality over time. The instruments are deployed for two to four weeks at a time, depending ',...
'on season, and measurements are taken every 30 minutes.  Currently one station on Prudence Island, ',...
'Potters Cove in the north has been established.   Potters Cove site, which was established in ',...
'December 1995 receives waste from boaters and is considered an impacted site.  All Rhode Island ',...
'State waters, however, were declared a federal no-discharge zone (for marine sewage) in late Spring ',...
'1998.  It is now illegal for boaters to discharge treated or untreated sewage into waters of the ',...
'state, including Potters Cove.');

Comments3 = sprintf('%s\n',...
'   ',...
'4.  Research Methods.',...
'   ',...
'Before each deployment, routine maintenance and calibration of the YSI instrument are carried out.',...  
'The instrument is cleaned to remove any fouling and the probes are checked for cracks or other ',...
'visible signs of damage.  O-rings are cleaned and greased, and batteries installed.  Calibrations ',...
'are performed for salinity, pH, dissolved oxygen, depth, and turbidity.  For the salinity ',...
'calibration, filtered seawater from Narragansett Bay is collected and its salinity determined using',... 
'an autosal.  This seawater is then used as a salinity standard. A two-point pH calibration is ',...
'performed using pre-made buffer solutions of pH 7 and 10 obtained from Fisher Scientific. Old pH ',...
'solutions are used for rinsing the probes.  The dissolved oxygen membrane is replaced 24 hours ',...
'prior to calibration.  The DO probe is then calibrated by placing a wet sponge in the calibration ',...
'cup and allowing the instrument to equilibrate as per the manufacturer''s instructions for 100% ',...
'air saturation calibration.  The depth sensor is calibrated to sea level with the sonde standing ',...
'up in air, calibration cup removed.  The turbidity sensor is calibrated with distilled water ',...
'(NTU = 0).  In August 1998, turbidity sensors were calibrated with distilled, deionized water ',...
'(0 NTU) and a standard diluted with distilled, deionized water to 10 NTU.  As  of December 28, ',...
'1998, a three point turbidity calibration was instituted (0, 10, 100 NTU).  ',...
'   ',...
'Currently only a northern site, Potters Cove, is being monitored. The sondes are deployed in PVC ',...
'tubes with sections cut out to allow water flow.  The PVC tube is attached to a dock.   The sondes ',...
'are programmed to collect data every 30 minutes during deployment.  Deployments generally last ',...
'two weeks to four weeks, data collection is continuous unless some mishap occurs.  At the end ',...
'of each deployment, the data is uploaded, put in Excel format, and QA/QC''d using the Excel Macros ',...
'provided by the CDMO.');

Comments4 = sprintf('%s\n',...
'    ',...
'5.  Site Location and Character.',...
'   ',...
'The NARNERR consists of 2200 acres of diverse estuarine and terrestrial habitats ranging from ',...
'deep water to salt marshes to forested uplands.  The land holdings include 60% of Prudence Island, ',...
'most of nearby Patience Island and all of Hope Island off the west shore of Prudence.  ',...
'The Reserve is located close to the geographical center of Narragansett Bay in Rhode Island.',...
'	Tidal range:  -0.2 to 1.7 meters MLW',...
'	Salinity:  15 to 32 ppt',...
'	Temperature:  -1.0 to 26 C',...
'	Province:  North temperate, Virginian bioregion',...
'	Lat. 41 38''30"    Long. 71 20''30"',...
'   ',...
'Specific characteristics of the Potters Cove site are:',...
'	Depth:  2.2 to 3.8 meters',...
'	Bottom habitat: Sand, silt, some organic mud',...
'	Pollutants:  Boaters'' wastes',...
'	Watershed:  Narragansett Bay, North Prudence (4801 square km) ',...
'	Location:  41 38''25"N, 71 20''28"W ',...
'   ',...
'Specific characteristics of the T-wharf site are:',...
'	Depth:  4 meters',...
'	Bottom habitat: sand and silt',...
'	Watershed:  Narragansett Bay',...
'	Location:  41 34''53"N, 71 19''18"W',...
'   ',...
'6.  Data Collection Period');

Comments5 = sprintf('%s\n',...
'    ',...
'Potters Cove data collection began December 3, 1995 and is ongoing.  T-wharf data collection ',...
'began September 1996 and terminated in January 1998 when the sonde and its mounting were lost ',...
'at sea.',...
'   ',...
'7.  Associated Researchers and Projects.',...
'   ',...
'There is a research grade meteorological station located approximately 200 yards from the ',...
'Potters Cove station.  Chris Turner, R. I. Department of Environmental Management, Water Resources',...
'Division, is currently collecting data.  Parameters measured include wind speed and direction, ',...
'air temperature, humidity, precipitation, and barometric pressure.',...
'   ',...
'II.  Physical Structure Descriptors ',...
'   ',...
'8.  Sensor specifications, range of measurements, units, resolution, and accuracy:',...
'   ',...
'YSI 6000 datalogger',...
'Variable Name  Range of Measurement (Units)   Resolution            Accuracy  ',...
'------------------------------------------------------------------------------------',...
'Temp           -5 to 45 ( C)                  0.01 C                +/-0.15C',...
'SpCOND         0-100 (mS/cm)                  0.01mS/cm             +/-0.5% of reading +0.001 mS/cm',...
'Salinity       0-70 Parts per thousand (ppt)  0.01ppt               +/-1.0% of reading or 0.1ppt, ',...
'                                                                    (whichever is greater)',...
'DO             0-200 (%air saturation)        0.1% @air saturation  +/-2% @air saturation',...
'DO             200-500 (% air saturation)     0.1% @air saturation  +/-6% @air saturation',...
'DO             0-20 (mg/l)                    0.01 mg/l             +/-0.2 mg/l',...
'DO             20-50 (mg/l)                   0.01 mg/l             +/-0.6 mg/l',...
'Depth(shallow) 0-9.1 (m)                      0.001 m               +/-0.018 m',...
'pH             2-14 units                     1.01 units            +/-0.2 units',...
'Turb           0-1000 (NTU)                   0.1 NTU               +/-5% of reading or 2 NTU (whichever is >)',...
'Date    1-12, 1-31, 00-99 (Mo,Day,Yr)    1 month, 1 day, 1 year',...
'Time    0-24, 0-60, 0-60 (Hr, Min, Sec)  1 hr, 1 min, 1 s');

Comments6 = sprintf('%s\n',...
'   ',...
'9.  Coded variable indicator and variable code definitions:',...
'   ',...
'Site definitions: PC = Potters Cove; TW = T-wharf.',...
'File definitions: YSI deployment site/month/year (ex: PC0196 = Potters Cove data from January of 1996)',...
'   ',...
'10.  Data anomalies.',...
'   ',...
'January, 1998:',...
'	PC:  No turbidity data were collected this month.  No alterations were made to the data, ',...
'no anomalies were noted.',...
'   ',...
'	TW:  Sonde was lost at sea on 12/30/97 and not recovered until late Fall 1998.  Data was ',...
'collected for a portion of January while the sonde, but is not reported here since it is not possible',... 
'to determine the unit''s exact location even though it evidently remained in the vicinity of the ',...
'T-Wharf where it was eventually recovered.',...
'   ',...
'February, 1998: ',...
'	PC:  No sonde deployed 2/20/98 11:30 hrs until 2/26/98 12:30 hrs.  No turbidty data collected ',...
'for whole month.  DO values noted as high, especially on 2/13/98 but were left in the data set.  ',...
'These DO values may be a result of fouling.  Did note that DO and temperature seemed to track from ',...
'2/26/98 to end of month, but again, no data were deleted.',...
'   ',...	 
'March, 1998:',...
'	PC: No turbidity data were gathered during the entire month.  No data anomalies noted, ',...
'no data deleted.');

Comments7 = sprintf('%s\n',...
'   ',...	 
'April, 1998:',...
'	PC:   No turbidity data were gathered during the entire month.  Missing 2 rows of data ',...
'(4/09/98 09:30 hrs and 10:00 hrs) between deployment of sondes.  DO values noted as high from ',...
'04/07/98 17:00 hr, but again left in.',...
'  ',...	 
'May, 1998:',...
'	PC:  Missing data between deployments 5/1/98 15:00 hr until 5/6/98 9:00 hr.  No turbidity ',...
'data taken for the whole month.  DO data seemed high on 5/16/98 through 5/19/98 but this was part ',...
'of a continuous deployment from 5/06/98 through end of month.  ',...
'   ',...
'June, 1998:',...
'	PC:  Begin turbidity probe deployment 6/05/98 with 1 point calibration (0 NTU); no turbidity ',...
'data prior to 06/05/98.   Puncture in DO membrane resulted in deletion of anomalous data from ',...
'6/20/98 19:00 hr through 6/26/98 7:30 hr.   Extreme negative turbidity value (-656) on 6/30/98 ',...
'17:30 hr deleted.  NB:  There were severe rains during this month resulting in a monthly total ',...
'of over 12.00 inches.  One rain storm left over 4 inches over the course of a weekend.  ',...
'   ',...
'July, 1998',...
'	PC:   Missing data between deployments:  7/24/98 9:00 hr and 7/24/98 9:30 hr.  High DO ',...
'values noted for 7/1/98 through 7/13/98;  values exceeded 200% saturation and were deleted.   ',...
'A clear puncture caused extreme DO values which were deleted from 7/23/98 00:00 hr until 7/24/98 ',...
'8:30 hr.  Large negative turbidity values were deleted on 7/3/98 17:00 hr (-81.9 NTU) and on ',...
'7/5/98 4:30 hr (-702.9 NTU).  From 7/13/98 through 7/24/98, sonde actually logged parameters at ',...
'9:52 minutes after the half hour.  ',...
'   ',...
'August, 1998:');

Comments8 = sprintf('%s\n',...
'	PC:  Several internal device errors occurred throughout deployment of sonde from 8/12/98 ',...
'through 8/24/98 possibly due to power supply malfunction.  This resulted in large gaps of missing ',...
'data.  However, consultation with YSI technical support indicated that the data that were collected ',...
'at this time should be of satisfactory reliability.  Data stream regained on 8/24/98 when a ',...
'different sonde was deployed.  DO membrane punctured 8/25/98 2:30 hr resulting in deletion of DO ',...
'data from that point through the end of the month.  Large negative turbidity value on 8/11/98 ',...
'13:30 hr. was deleted.  ',...
'   ',...
'September, 1998:',...
'	PC:  Several rows of data were not gathered due to gaps in deployment:  on 9/9/98 at 6:30 ',...
'hr through 9:00 hr. and on 9/23/98 at 8:30 hr and 9:00 hr.  Despite use of three different sondes ',...
'through the course of the month, punctures or other problems developed so that DO data collected ',...
'was significantly above realistic levels (e.g. 400%).  As a result of these difficulties, all DO ',...
'data collected for the month was deleted.  :( ',...
'    ',...
'October, 1998:',...
'	PC:  Missing data for 10/28/98  9:00 hr. as a result of deployment mismatch.  DO data deleted ',...
'from 10/1/98 through 10/12/98 7:30 hr since this was the same sonde deployment continued from ',...
'September.  See September 1998 data anomaly section for full explanation.  ',...
'   ',...
'November, 1998',...
'	PC:  Power malfunction in sonde for deployment of 11/18/98 through end of month.  No data ',...
'collected for this period.  :(  Low DO values noted for 11/5/98, but not deleted since these data ',...
'were from one sonde deployed continuously from 10/28/98 through 11/18.  ',...
'   ',...
'December, 1998',...
'	PC:  Power malfunction in sonde for deployment 12/01/98 through 12/2/98 14:30 hr., no data');

Comments9 = sprintf('%s\n',...
'obtained for this period.  Negative turbidity values (-1 NTU when rounded) occurred at the following ',...
'times and were converted to 0 values:  12/30/98 from 10:30 hr through 21:00 hr; 12/31/98 00:00 hr ',...
'through 8:00 hr and 10:30, 11:00, 12:00, 12:30, 15:00, 15:30, 16:30, 17:30, 18:30, 19:30, 20:00, ',...
'21:00 and 22:00 through 23:30 hr.',...
'   ',...
'11.  Missing Data',...
'   ',...	
'January, 1998:',...
'	PC:  No turbidity data were collected this month.',...
'   ',...
'	TW:  Sonde was lost at sea on 12/30/97 and not recovered until late Fall 1998.  Data was ',...
'collected for a portion of January while the sonde, but is not reported here since it is not possible',... 
'to determine the unit''s exact location even though it evidently remained in the vicinity of the ',...
'T-Wharf where it was eventually recovered.',...
'   ', ...
'February, 1998: ',...
'	PC:  No sonde deployed 2/20/98 11:30 hrs until 2/26/98 12:30 hrs.  No turbidty data ',...
'collected for whole month.',...
'   ',...	 
'March, 1998:',...
'	PC: No turbidity data were gathered during the entire month.	 ',...
'   ',...
'April, 1998:',...
'	PC:   No turbidity data were gathered during the entire month.  Missing 2 rows of data ',...
'(4/09/98 09:30 hrs and 10:00 hrs) between deployment of sondes. ',...
'   ',...
'May, 1998:',...
'	PC:  Missing data between deployments 5/1/98 15:00 hr until 5/6/98 9:00 hr.  No turbidity ',...
'data taken for the whole month ',...
'   ',...
'June, 1998:');

Comments10 = sprintf('%s\n',...
'	PC: No turbidity data prior to 06/05/98.   Puncture in DO membrane resulted in deletion of ',...
'anomalous data from 6/20/98 19:00 hr through 6/26/98 7:30 hr.   Extreme negative turbidity value ',...
'(-656) on 6/30/98 17:30 hr deleted. ',...
'   ',...
'July, 1998',...
'	PC:   Missing data between deployments: 7/24/98 9:00 hr and 7/24/98 9:30 hr.  High DO ',...
'values noted for 7/1/98 through 7/13/98; values exceeded 200% saturation and were deleted.   A ',...
'clear puncture caused extreme DO values which were deleted from 7/23/98 00:00 hr until 7/24/98 ',...
'8:30 hr.  Large negative turbidity values were deleted on 7/3/98 17:00 hr (-81.9 NTU) and on 7/5/98 ',...
'4:30 hr (-702.9 NTU).',...
'    ',...
'August, 1998:',...
'	PC:  Several internal device errors occurred throughout deployment of sonde from 8/12/98 ',...
'through 8/24/98 possibly due to power supply malfunction.  This resulted in large gaps of missing ',...
'data.  DO membrane punctured 8/25/98 2:30 hr resulting in deletion of DO data from that point ',...
'through the end of the month.  Large negative turbidity value on 8/11/98 13:30 hr. was deleted.  ',...
'   ',...
'September, 1998:',...
'	PC:  Several rows of data were not gathered due to gaps in deployment -- on 9/9/98 at ',...
'6:30 hr through 9:00 hr. and on 9/23/98 at 8:30 hr and 9:00 hr.  Despite use of three different ',...
'sondes through the course of the month, punctures or other problems developed so that DO data ',...
'collected was significantly above realistic levels (e.g. 400%).  As a result of these difficulties,',... 
'all DO data collected for the month was deleted.  ',...
'    ',...
'October, 1998:',...
'	PC:  Missing data for 10/28/98  9:00 hr. as a result of deployment mismatch.  DO data ',...
'deleted from 10/1/98 through 10/12/98 7:30 hr since this was the same sonde deployment continued ',...
'from September.  See September 1998 data anomaly section for full explanation.  ',...
'   ',...
'November, 1998');

Comments11 = sprintf('%s\n',...
'	PC:  Power malfunction in sonde for deployment of 11/18/98 through end of month.  ',...
'No data collected for this period.  ',...
'   ',...
'December, 1998',...
'	PC:  Power malfunction in sonde for deployment 12/01/98 through 12/2/98 14:30 hr., ',...
'no data obtained for this period. ',...
'    ',...
'12.  Other Remarks/Notes',...
'	Probe failures have resulted in the loss of much dissolved oxygen and turbidity data, ',...
'particularly in the summer.  Membrane puncture during deployment has also caused losses in DO data.',...
'We are currently working on ways to more effectively keep animals out of the probe guards.  ',...
'Meshes used to date seem only to trap animals once they get past the mesh.');

Comments = [Comments1 Comments2 Comments3 Comments4 Comments5 Comments6 Comments7 Comments8 Comments9 Comments10 Comments11];


