The following files are now available online under 'Files as received', unprocessed by the CCHDO.

Tritium Submission.xlsx

The following files are now available online under 'Files as received', unprocessed by the CCHDO.

Jenkins_325020060213-p16-2006_Get_RH5_Helium_Results.xlsx

Mercury data resubmitted via email from David Krabbenhoft to Susan Piercy with station, cast and bottle information as well as added quality flags.

The pH quality flag for station 40, cast 1, bottle 13 was changed from 2 to 3.
The Alkali quality flag for station 14, cast 1, bottle 32 was changed from 2 to 3.
These new values are reflected in the woce, exchange, and netCDF formats.

Merging notes for p16n_325020060213 bottle file merge of DOC and TDN
submitted on 2009.11.20 by Alex Kozyr.  Data from Dennis Hansell.


Made following edits to file p16N_2996_DOC_TDN_20091120.csv

-Removed all extra commas from lines
-Edited expocode from scientific notation to the integer
expocode 215020060213.
-Edited parameter header PH_TEMP to PH_TMP.
-Edited file called p16N_2996_DOC_TDN_20091120_edt.csv

Used merge_exchange_bot.rb to merge both DOC, TDN and their respective
flag values.  no errors were encountered.

Converted output file to woce format and netcdf format with no errors
encountered.  Could not format check the woce formatted file however,
due to the large number of total parameters as well as the unrecognized
post-WOCE parameters.

Checked the exchange file with the online bottle compare tool and
netCDF files in JOA.  No errors were found.

renamed current files and moved them to the original directory.
Placed all newly merged files online and ran the cchdo_update.rb.
Sent notes file to Jerry.

 We aren't able to merge by USGS bottle ID, location, and time.  It would make it much easier to merge data if they were identified by (station, cast, sample or bottle number).
  Also, quality information on this data set we would be useful.

We have discovered a calibration problem with the del 13C data from
CLIVAR P16S and P16N. It is possible that the problem exists with
other cruises.

The C13 data have already been submitted to CCHDO and to CDIAC. I just
checked and it appears that only the P16S data are posted, and only at
CCHDO.

The 13C data are used in the calculation of D14C, however the
magnitude of the 13C calibration problem is small enough that the
effect on the D14C will be negligible.

What to do:
CCHDO - please remove the posted 13C data for P16S and do not post
those for P16N. The D14C data for P16N can be posted. Please add a
note to the "Data History" stating that the data for P16S were
removed. Another note will be needed once the corrected data are
available. This is not a proprietary data issue, we just don't want a
copy of the data that is known to need calibration in circulation.

CDIAC - the text for the printed NDP will state the 13C problem. Once
the problem is solved, we will submit the corrected 13C data and
replacement text for the on-line version of the NDP. We will want to
add a note to the data-download web page so that any end user will
know what they are getting. Your online data files need the C14 for
both cruises.

10.27.2008  DBK
Merging Notes for P16N_2006a (325020060213) Bottle file:

in 04.2007, final CFC's were sent into CCHDO, but were
missed during the merging process.  THese values were
merged using JOA with no apparent errors, however because
the JOA merge tool is still in testing, the values were
also merged by hand and the files were checked against
e/o.  Because JOA did not appear to be merging correctly,
mrgsea output file was used as final merged file.  JOA
bugs will need to be brought to Oz.  Following notes
are from the merge process using mrgsea:

Parameters merged were:
CFC_11, CFC_12 and CFC113 and their respective flag
values.
mrgsea was used to merge these values.  The following
station/cast/sample combinations contained incorrect
flags and were edited in the input file before being
merged:
52/2/4  CFC11 value 0.000 flag 0, edited to flag 2
51/1/18 CFC12 value 0.000 flag 0, edited to flag 2
53/1/10 CFC12 value 0.000 flag 0, edited to flag 2
53/1/16 CFC12 value 0.000 flag 0, edited to flag 2
54/1/11 CFC12 value 0.000 flag 0, edited to flag 2
54/1/15 CFC12 value 0.000 flag 0, edited to flag 2
given the surrounding CFC values, the values of 0.000
were assumed to be valid measurements and therefore,
the incorrect WOCE flag of "0" was edited to "2" to
reflect a valid data value.

No errors were reported during the merge process.
Output file was checked with wocecvt, no errors reported.
Exchange and netcdf files were created with no errors.

Final files in this directory are called:
p16n_2006ahy_10.31.2008.txt
p16n_2006a_hy1_10.31.2008.csv
p16n_2006a_nc_hyd_10.31.2008.zip

These files were renamed to the correct CCHDO file names
and copied to the parent directory for this cruise.
web_update.rb was run and 00_README file was emailed to
Jerry.

Mary Johnson pointed out that the txt document for this cruise was one line, and contained unprintable characters.  This has now been corrected.

BrdU 11-16-07.txt Type:  Status: public
Name: Carlson, Craig
Institute: uCSB
Country: uSA
Expo:P16N_325020060213 Line: P16N
Date: 2006-02-01 
Action:Merge Data
Notes:These data are Bacterial Production data as measure by bromodioxyuridine (BrdU) incorporation.  These data are ancillary to the core CDOM data set already submitted.

Type:  Status: public
Name: Kozyr, Alex
Institute: CDIAC/ORNL
Country: USA
Expo:325020060213   Line: P16N_2006
Date: 2006-02-13 
Action:Merge Data, Place Online, Updated Parameters
Notes:Please, merge these new CO2-related parameters. Note, that PCO2 replaced with FCO2 header and FCO2_TMP column is added. Also, there will be just one pH column (previously there were 2 columns for UM and USF measurements). The pH column header should have the pH scale name, as it is on this case pH on the total scale and consists of UM measurements on leg 1 and USF measurements on leg 2. There is also an additional column pH_TMP for pH temperature.

Notes on creating netcdf CTD files for p16n_2006 (3250200602)

Two copies of CTD data exist for this cruise.  One set submitted
by Kristy McTaggart in 02/2006.  These data are in WOCE format.
The other set containing additional data was obtained by Steve Diggs
from NOAA on 03/30/2006 .  These data are in .csv format.  For the
purposes of converting to netcdf, the .csv format files were used
since they had a later version date than those in WOCE format submitted
by Kristy McTaggart.

The WOCE formatted files will be zipped but not placed online.  At
this time we do not have software that will back-format a .csv foramtted
file to WOCE format.  Therefore the WOCE files remain an earlier version
of the CTD data.  They will reside in the original directory.

The CTD data in .csv format included data for the following parameters:

CTDPRS and FLAG, CTDTMP and FLAG, CTDSAL and FLAG, CTDOXY and FLAG,
CTDNOBS, CTDETIME, TRANSM and FLAG, FLUORM and FLAG

These files were renamed according to CCHDO file name convention and
zipped together with the citation information file and placed back online.

These files however would not pass through the conversion code to
generate netcdf files.  Therefore the following parameters were
removed from the .csv files for the purposes of generating netcdf files:

CTDNOBS, CTDETIME, TRANSM and FLAG, FLUORM and FLAG

Netcdf CTD files were then generated with no errors.  Files were
renamed to follow cchdo file naming conventions, zipped along with
the citation information file and placed online.

05.21.2007  DBK
Merging Notes for P16N_2006a (325020060213) Bottle file:

Merged the following parameters:

From Alex Kozyr:
Total Carbon, Alkalinity, PCO2@20, pH (UM)
Original ODF bottle file had no quality byte for pco2_20, so
this byte was inserted into the QUALT1 word.
No problems were encountered with the merging of these data.

From Dennis Hansell:
DOC
These data were also included in the file sent by Kozyr, however
at Kozyr's direction, file from Hansell was used instead of the
Kozyr file's values.
No problems were encountered with the merging of these data.

From Chris Langdon:
bottle O2
These data were also included in McTaggart file however at
the direction of McTaggart the Langdon file's values were
used.
No problems were encountered with the merging of these data.

From Kristy McTaggart:
CTD salinity, CTD oxygen, Bottle salinity
No problems were encountered with the merging of these data.

From Fred Menzia:
Phosphate, silicate, nitrate, nitrite.
Station 84, cast 1, sample 11 for phosphate had an incorrect
flag of zero (0).  There appeared to be a valid data value
present, so the flag was changed to a "2".  This will be
communicated to data PI for comment.

Entire file:
-changed expocode from 33ATAT-13 to 325020060213.
-Because various data PI's used a mixture of missing values
(-9, -9., -999.) all missing values were edited to -9. where
precision matched the precision of corresponding data measurement.
-The following headers were changed to conform to WOCE standards:
CFC-113 to CFC113
PCO2_T to PCO2TMP
-Other edits may be performed to headers as discussion continues
on NON-WOCE header mnemonics.
-added name/date stamp.

Merging Notes for P16N_2006a (325020060213) summary file:

-changed expocode from 33ATAT-13 to 325020060213.
-added name/date stamp.

File: Extcfcs4whpo.senttoWOCE_9april2007  Type: ASCII Status: Public
Name: Bullister, John 
Institute: NOAA-PMEL 
Country: USA
Expo:33ATAT-13 Line: P16
Date: 02/2006
Action:Merge Data,Place Data Online
Notes:
Replace all CFC-11, CFC-12 and CFC-13 values (and flags) with data in attached file.
Concentrations are reported on SIO98 calibration scale and are in pmol/kg
Upload directory: /incoming_data/20070409.174839_P16_Bullister,_John

There are currently 4 docs in the p16n_2006a directory:

  p16n_2006ado.pdf (leg 1)
  p16n_2006ado.text (leg 1)
  p16n_2006a2do.pdf (leg 2)
  p16n_2006a2do.text (leg 2)

these should all be retired to the old docs or original directory and replaced by:

  p16n_2006ado.pdf (both legs)
  p16n_2006ado.txt (both legs)

which you'll find in my home directory

Fred (Menzia) just phoned me and said that he had found a couple of formatting errors in Excel after sending the initial email.  He will fix those and try the submit process.

The CCHDO completely understands that we obtain only carbon-related parameters from Alex at CDIAC and do not rely on CDIAC to provide any other hydrographic parameters nor to verify the pedigree of any data fileor parameters other than those carbon-related.

This is why we take the files from CDIAC and extract only carbon parameters to merge into our current bottle file.

Because of this relationship, neither CDIAC nor the CCHDO has a clear pedigree for the P16N_2006 (3250200602) bottle file.  We understand that we now have at the CCHDO final TALK, TCO2, pH, pCO2 and DOC as well as final O2 data just now sent from Langdon.

What we do not have is an updated bottle file in which to merge these parameters (meaning: station, cast, bottle, sample, press, salts, oxy, nuts).  We are looking to Dr.s Sabine and Feely for direction in this matter.  We can certainly merge CDIAC's final data into the bottle file originally sent in 05/2006, but if there was some concern regarding the quality of those data we would appreciate clarification and instruction.

Thanks to all in sorting this matter out.  We hope to resolve these issues and expedite the merging of these parameters in order to get P16N online as soon aspossible.

Regarding the final word in carbon parameters from Alex (1/18/2007).  This is the file I will use to merge all updated carbon data into the p16N bottle file. 

I think you are talking about different things. CDIAC is only responsible for the carbon-related data not hydrographic or other chemical data. All carbon data submitted to CDIAC are final (declared by PIs) and submitted to CCHDO. I have no idea about other data if it is preliminary or final. I can see from Dick's message to Steve that there are some problems with data, but it is not clear what kind of data. I've never received any messages about any problems for carbon data after I submitted these data to CCHDO. So, to be clear from my side: I don't know anything about hydrographic and other chemical data; at this point all CO2-related data at CDIAC with "final and public" status and submitted to CCHDO: 
http://cdiac.ornl.gov/oceans/RepeatSections/clivar_table_inv.html (see P16N_2006).

Apologies if this has been resolved already....if not, here's my 2 cents.  I don't know if the Oxygen data from Chris Langdon is the same or different then the bottle file Alex received.

What I can easily determine is the following: When I open Alex's data file from here:
http://cdiac.ornl.gov/ftp/oceans/CLIVAR/P16N_2006.data/p16n_2006a_hy1.csv and compare that file to what Chris sent to me and I forwarded to you, all the Oxygen data appears to be the same. However, there are 44 values where the quality control flags have changed.

Since Chris Langdon is the PI for the Oxygen measurements on this cruise...I would use the file he sent to me and I forwarded on to you. As the date of this file is November 28th, I would logically infer it is the same file that he unsuccessfully attempted to submit via the cchdo web site.

Apologies for the confusion. Hopefully this is now sorted out. I would merge Chris Langdon's Oxygen csv file unless he replies to this message with conflicting information.

All of our latest data have been submitted to CDIAC. Please work with Alex Kozyr to ensure that your files agree with what was sent to him. Please let us now if there are any questions or problems that arise.

John and I were each the lead CFC analyst on one of the two legs of P16N repeat. We used the same equipment and software, but have been trying to identify an apparent offset between the data sets depending on who did the processing (same software, same data, slightly different values). We finally have tracked the problem to a unreported feature (bug) in the data processing software. We installed the fix this week and should be able to report the final values before the end of the month.

File: p16N-DOC-subm-1106.csv  Type: ASCII Status: Public
Name: Kozyr, Alex 
Institute: CDIAC/ORNL 
Country: USA
Expo:3250200602 Line: P16N_2006
Date: 02/2006
Action:Merge Data,Place Data Online
Notes:

File: p16n_allf.flg  Type: ASCII CTDO discrete data Status: Public
Name: McTaggart, Kristy 
Institute: NOAA PMEL 
Country: USA
Expo:33TT200601 Line: P16N
Date: 02/2006
Action:Merge Data,Place Data Online,Updated Parameters
Notes:
  Calibrated CTDO bottle data with ammended sample salinity flags.
  87 profiles in ASCII format
  1 file of calibrated discrete CTDO data and ammended sample salinity flags
  1 documentation file and 4 .pdf figures

 I do anticipate a final update to the CFC data. I suspect it will  be completed in mid-October.

Here is attached the final carbon data (TCO2, TALK, pCO2, and pH) and quality flags for Repeat hydrography cruise P16N_2006, EXPOCODE  3250200602. The data are in the  exchange formatted file. Please merge these data into the final hydrography file. Could you please let me know when the data will be merged.

We've finally removed the offending parameters from the bottle file.  Actually, just 'parameter', since PH from the two institutions was all that needed removing. TALK and DIC were not in this version of the Exchange bottle file

The webpage reflects this change:

	http://cchdo.ucsd.edu/data/co2clivar/pacific/p16/p16n_2006a/

Please let me know if the are questions, comments or concerns.  Once we receive the sanctioned versions of TALK,PH and DIC, we will merge them into the online bottle file and replace the one currently online.

I knew there were some issues with the pH data, I wasn't aware that you had concerns over the TALK data as well.  By copy of this e-mail I will ask Susan not to post the TALK and pH data on the website until she hears back from you.

I just put pdf and text docs for the p16n_2006a cruises (both legs) in my directory.  Please put them online when possible.

Here you go!  Let me know if there are any problems.  I only have the data in WHP-Exchange (csv) format.  

As of Sunday morning (9:00am PDT) I have removed all links to the bottle data for P16n as you have requested.  Only the SUM, CTD and DOC links remain.  Also, I've updated the contact information regarding Chief Scientists to include both of your names and contact information.  My apologies, that link wasn't made active, but it was there.

This brings up an interesting dilemma pertaining to the de facto bylaws for the US Repeat Hydrography Program.  I think that there was a deadline for getting these data to the data center by a certain date, but nothing that says the the files need to be >available< to the public.

For now, please check the website and determine if you are all comfortable with the data that are available and the accuracy of the information provided on the webpage.  If there are any additional changes or updates, please feel free to let us know.

The preliminary data for P16N from 2006 (3250200602) are now available on the CCHDO website:

	http://cchdo.ucsd.edu/data/co2clivar/pacific/p16/p16n_2006a/index.htm

	(WOCE-SUM, Bottle & CTD in Exchange format as well as pdf documentation)

These data are also available through the website through the normal means of discovery.  For now, the cruise report on reflects the events pertaining to Leg 1, though I believe that the information for Leg 2 is available.

NetCDF files will be available later next week. 

As you know, I recently returned from the first leg of the P16N cruise on the Thomas G. Thompson. The cruise went very well. Attached, please find a copy of my preliminary cruise report. Please let me know if you have any questions or concerns with this report. Frank Delahoyde provided me with a DVD of the shipboard data. I presume he will deliver the data to Scripps.

You can find the cruise web site at the following address:

http://www.pmel.noaa.gov/co2/p16n/

However, I don't think you will find the information you are looking for yet. The cruise track that is shown at the site is not the final track. The final track is not set yet because we are still negotiating with the ship to determine whether we are doing a port stop in Hilo or Honolulu. The cruise personnel are not finalized either. We are told that there are 35 berths and at the moment we have 37 people that want to go on each leg. We are negotiating with the groups to get this number down. We just designated the student participants last Friday. I think we will have a much better idea next week if you can wait that long. I will let you know once we have these things better nailed down.