Files in the Dataset have been checked for format consistency, and merged into a single, integrated, downloadable file.
Download Entire Dataset Submit Data For This Cruise How to Cite DatasetFiles listed here may be useful and are provided 'as is'. Files might include raw data, intermediate processing, or other data collected on a cruise that is outside the current scope of CCHDO.
| Role | Data Type | Format | Filename (Download) |
|---|---|---|---|
| ancillary | bottle | 325020060213_mercury_data.xls (211.5 kB) |
Files listed here are the most recent version submitted by the cruise scientists, but have not yet been checked for consistency and merged into the main Dataset. They are provided "as is". If you are unsure of which files to use, stick to the Dataset files above.
These files are not yet in the Dataset.
| Filename (Download) | Size | Date Submitted |
| CCHDO-2011-09-06.txt | 12.3 kB | 2011-12-19 |
CCHDO-1.0 CF netCDF files converted from bottle exchange file
CCHDO-1.0 CF netCDF files converted from ctd exchange file
P16N 2006 325020060213 processing - CTD merge CTDBEAMCP into existing Exchange file
2017-11-08
CCHDO
Submission
filename submitted by date id
------------ ------------ ---------- -----
2006P16N.TXT Wilf Gardner 2017-06-01 12775
p16n.zip Wilf Gardner 2009-05-22 8500
Changes
-------
p16n_2006a_ct1.zip, renamed 325020060213_ct1.zip
- changed file names to conform to Exchange format
- merged CTDBEAMCP data from Wilf Gardner
- station 58, cast 1 has no CTDBEAMCP data, used fill values
- removed TRANSM and TRANSM_FLAG_W, no longer needed since CTDBEAMCP is available
- changed FLUORM to CTDCDOMFRAW
- changed FLUORM_FLAG_W to CTDCDOMFRAW_FLAG_W
- changed EXPOCODE from 3250200602 to 325020060213
- added header and unit comments
- added cruise comments
p16n.zip
- moved previous CTDBEAMCP data submission to Data History because an updated version was submitted.
Conversion
----------
file converted from software
--------------------- ------------------ -----------------
325020060213_nc_ctd.zip 325020060213_ct1.zip 0.8.2-48-g594e1cb
Updated Files Manifest
----------------------
file stamp
--------------------- ----------------
325020060213_ct1.zip 20171108CCHSIO
325020060213_nc_ctd.zip 20171108CCHSIO
:Removed parameters: TRANSM, TRANSM_FLAG_W
:Updated parameters: none
:Merged parameters: CTDBEAMCP, CTDBEAMCP_FLAG_W
opened in JOA with no apparent problems:
325020060213_ct1.zip
325020060213_nc_ctd.zip
opened in ODV with no apparent problems:
325020060213_ct1.zip
As confirmed by Wilf Gardner and Alexey Mishonov the text related to transmissometer pathlength has been changed from 0.1m to 0.25m.
As confirmed by Wilf Gardner and Alexey Mishonov the text related to transmissometer pathlength has been changed from 0.1m to 0.25m.
includes station information
P16N 2006 325020060213 processing - BTL/merge - TRITUM
2017-07-20
C Berys
Submission
filename submitted by date id
----------------------------------------------------------------------------------
WHOI P16_2006 Revised Tritium Submission.xlsx William Jenkins 2015-11-30 12039
325020060213.exc.csv Bob Key 2015-12-17 12050
WHOI P16_2006 Revised Tritium Submission V2.xlsx Bob Key 2017-07-20 13553
Changes
* none
Merge
WHOI P16_2006 Revised Tritium Submission V2.xlsx merged into 325020060213.exc.csv by Bob Key.
325020060213.exc.csv merged into 325020060213_hy1.csv using hydro 0.8.2-48-g594e1cb.
:Updated Parameters: TRITUM TRITER TRITUM_FLAG_W
325020060213_hy1.csv opened in JOA with no apparent problems.
Conversion
----------
file converted from software
--------------------------------------------------------------------
325020060213_nc_hyd.zip 325020060213_hy1.csv hydro 0.8.2-48-g594e1cb
325020060213hy.txt 325020060213_hy1.csv hydro 0.8.2-48-g594e1cb
Updated Files Manifest
----------------------
file stamp
-------------------------------------------
325020060213_hy1.csv 20170720CCHSIOCBG
325020060213_nc_hyd.zip 20170720CCHSIOCBG
325020060213hy.txt
Wilf Gardner's CTDBEAMCP final data to merge
325020060213.exc.csv available as received, submitted 2015-12-17 by Robert Key
File contained revised H3 data submitted recently by W. Jenkins.
File contained revised H3 data submitted recently by W. Jenkins. Also, this file needs to be checked carefully. I think is has HPLC pigment values. If correct, the parameter names and units need to be checked against the newly "set" names (from SOCCOM work/cruises). System Message: Submitter requests file be attached to cruise 433
WHOI P16_2006 Revised Tritium Submission.xlsx available as received, submitted 2015-11-30 by William Jenkins
Submission note: This is a resubmission of tritium data from the WHOI lab. The previously submitted data are in error due to a software bug.
This is a re-submission of tritium data for this cruise to replace previous tritium data which is erroneous. System Message: Submitter requests file be attached to cruise 433
P16N 2006 325020060213 processing - BTL/merge - TRITUM
2015-05-27
C Berys
Submission
filename submitted by date id
---------------------------------------------------------------------
LDEO_NGL_CliVarTritium4CCHDO_P16S.xlsx Robert Newton 2015-04-13 1250
325020060213.exc.csv Robert Key 2015-04-15 455
Merge
LDEO_NGL_CliVarTritium4CCHDO_P16S.xlsx
325020060213.exc.csv
Merged 325020060213.exc.csv into 325020060213_hy1.csv using hydro 0.8.2-40-g569f4c2.
:New parameters: TRITUM, TRITUM_FLAG_W, TRITER
All comment lines from original file copied back in following merge. 320620140320_hy1.csv opened in JOA with no apparent problems.
Conversion
----------
file converted from software
--------------------------------------------------------------------
325020060213_nc_hyd.zip 325020060213_hy1.zip hydro 0.8.2-40-g569f4c2
325020060213hy.txt 325020060213_hy1.csv hydro 0.8.2-40-g569f4c2
Updated Files Manifest
----------------------
file stamp
-----------------------------------------
325020060213_hy1.csv 20150527CCHSIOCBG
325020060213_nc_hyd.zip 20150527CCHSIOCBG
325020060213hy.txt
There is not enough information to know where this file should go in the timeline.
There is not enough information to know where this file should go in the timeline.
There is not enough information to know where this file should go in the timeline.
There is not enough information to know where this file should go in the timeline.
There is not enough information to know where this file should go in the timeline.
There is not enough information to know where this file should go in the timeline.
There is not enough information to know where this file should go in the timeline.
There is not enough information to know where this file should go in the timeline.
The following data are now available As Received, unprocessed by the CCHDO.
http://cchdo.ucsd.edu/cruise/325020060213
325020060213.exc.csv
Expocode: 325020060213 Ship: None Woce Line: P16N Note: Merge of LDEO H3 values. LDEO He data and WHOI H3 & He data had been previously merged. There were no common samples, so no issues with the merges.
Expocode: 325020060213 Ship: None Woce Line: P16N Note: Tritium measurements from the P16N repeat hydro cruise.
The following data are now available As Received, unprocessed by the CCHDO.
http://cchdo.ucsd.edu/cruise/325020060213
LDEO_NGL_CliVarTritium4CCHDO_P16N.xlsx
He/Ne
=======================
325020060213 processing
=======================
2014-09-26
A Barna
.. contents:: :depth: 2
Submission
==========
================================ ============= ========== ========= ====
filename submitted by date data type id
================================ ============= ========== ========= ====
P16N_2006_LDEO_NGL_HeNeData.xlsx Robert Newton 2014-09-25 He/Ne 1219
================================ ============= ========== ========= ====
Parameters
----------
P16N_2006_LDEO_NGL_HeNeData.xlsx
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
HELIUM [1]_ [4]_
DELHE3 [1]_ [4]_
NEON [1]_ [3]_ [4]_
NEONER [3]_ [4]_
DELHER [4]_
He4ccSTPg [3]_
He4ErccSTPg [3]_
HELIER [4]_
NeccSTPg [3]_
NeErccSTPg [3]_
.. [1] parameter has quality flag column
.. [2] parameter only has fill values/no reported measured data
.. [3] not in WOCE bottle file
.. [4] merged, see merge_
Process
=======
Changes
-------
P16N_2006_LDEO_NGL_HeNeData.xlsx
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
onverted to csv using LibreOffice 4.3.0.4, changed column names to match CCHDO parameter list.
.. _merge:
Merge
-----
P16N_2006_LDEO_NGL_HeNeData.xlsx
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Merged using libcchdo version c516356
Directories
===========
:working directory:
/data/co2clivar/pacific/p16/p16n_2006a/original/2014.09.26_BTL_AMB
:cruise directory:
/data/co2clivar/pacific/p16/p16n_2006a
Updated Files Manifest
======================
================== =================
file stamp
================== =================
p16n_2006a_hy1.csv 20140926CCHSIOAMB
================== =================
He, d3He, Ne data from the Schlosser lab. Concentration data are in both ccSTP/g (used in our lab) and nMol/Kg (WOCE reporting standard, I think). 3HE/4He ratio is reported as d3He: percent difference from the ratio in air (which is 1.384 e-6).
Expocode: 325020060213 Ship: Thompson Woce Line: P16N Note: He, d3He, Ne data from the Schlosser lab. Concentration data are in both ccSTP/g (used in our lab) and nMol/Kg (WOCE reporting standard, I think). 3HE/4He ratio is reported as d3He: percent difference from the ratio in air (which is 1.384 e-6). Contact is Bob Newton: 845-365-8686 (office), 201-679-0263 (cell).
He, d3He, Ne data from the Schlosser lab. Concentration data are in both ccSTP/g (used in our lab) and nMol/Kg (WOCE reporting standard, I think). 3HE/4He ratio is reported as d3He: percent difference from the ratio in air (which is 1.384 e-6).
Contact is Bob Newton: 845-365-8686 (office)
The following files are now available online under 'Files as received', unprocessed by the CCHDO.
P16N_2006_LDEO_NGL_HeNeData.xlsx
Tritium Data
HELIUM/NEON
==================================================================
325020060213 processing - BTL/merge - HELIUM, NEON, DELHE3, TRITUM
==================================================================
2014-01-21
C Berys
.. contents:: :depth: 2
Submission
==========
========================================================= ================= ========== ============ ===
filename submitted by date data type id
========================================================= ================= ========== ============ ===
Jenkins_325020060213-p16-2006_Get_RH5_Helium_Results.xlsx William J Jenkins 2012-12-28 HELIUM/NEON 940
Tritium Submission.xlsx William J Jenkins 2013-01-14 Tritium Data 946
========================================================= ================= ========== ============ ===
Parameters
----------
Jenkins_325020060213-p16-2006_Get_RH5_Helium_Results.xlsx
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
- HELIUM [1]_ [4]_
- DELHE3 [1]_ [4]_
- NEON [1]_ [3]_ [4]_
- NEONER [3]_ [4]_
- HELIER [4]_
- DELHER [4]_
Tritium Submission.xlsx
~~~~~~~~~~~~~~~~~~~~~~~
- TRITUM [1]_ [4]_
- TRITER [4]_
.. [1] parameter has quality flag column
.. [2] parameter only has fill values/no reported measured data
.. [3] not in WOCE bottle file
.. [4] merged, see merge_
Process
=======
Changes
-------
.. _merge:
Merge
-----
Jenkins_325020060213-p16-2006_Get_RH5_Helium_Results.xlsx
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Merged Jenkins_325020060213-p16-2006_Get_RH5_Helium_Results.xlsx into p16n_2006a_hy1.csv using hydro 0.8.0-90-g3f58792.
:New parameters: HELIUM HELIUM_FLAG_W HELIER NEON NEON_FLAG_W NEONER DELHE3 DELHE3_FLAG_W DELHER
Tritium Submission.xlsx
~~~~~~~~~~~~~~~~~~~~~~~
Merged Tritium Submission.xlsx into p16n_2006a_hy1.csv using hydro 0.8.0-90-g3f58792.
:New parameters: TRITUM TRITER TRITUM_FLAG_W
All comment lines from original file copied back in following merge. p16n_2006a_hy1.csv opened in JOA with no apparent problems.
Conversion
----------
===================== ================== =======================
file converted from software
===================== ================== =======================
p16n_2006a_nc_hyd.zip p16n_2006a_hy1.csv hydro 0.8.0-90-g3f58792
p16n_2006ahy.txt p16n_2006a_hy1.csv hydro 0.8.0-90-g3f58792
===================== ================== =======================
All converted files opened in JOA with no apparent problems.
Directories
===========
:working directory:
/data/co2clivar/pacific/p16/p16n_2006a/original/2014.01.21_HELIUM-NEON-TRITIUM_CBG
:cruise directory:
/data/co2clivar/pacific/p16/p16n_2006a
Updated Files Manifest
======================
===================== =================
file stamp
===================== =================
p16n_2006a_nc_hyd.zip 20140121CCHSIOCBG
p16n_2006a_hy1.csv 20140121CCHSIOCBG
p16n_2006ahy.txt
===================== =================
=============================
325020060213 processing - BTL
=============================
2014-01-10
R Lee
.. contents:: :depth: 2
Process
=======
Changes
-------
- Added instructions for data citation
Conversion
----------
===================== ================== =======================
file converted from software
===================== ================== =======================
p16n_2006a_nc_hyd.zip p16n_2006a_hy1.csv hydro 0.8.0-81-gc0a14ea
===================== ================== =======================
All converted files opened in JOA with no apparent problems.
Directories
===========
:working directory:
/data/co2clivar/pacific/p16/p16n_2006a/original/2014.01.10_Citation_RJL
:cruise directory:
/data/co2clivar/pacific/p16/p16n_2006a
Updated Files Manifest
======================
- p16n_2006a_nc_hyd.zip
- p16n_2006a_hy1.csv
Clearly something is wrong with the nitrate for this sample (Nitrate = 0 at 58-1-18); we don't know what. In my copy of the data file I have replaced the "0" nitrate concentration with NA (-999) and changed the QF to 5. Any of the other choices (-999/9; 0/4;etc.) would work as well for most software, but the -999/5 is probably best. Odds are this was a clerical error of some sort. I can't think of anything that would change this unless Calvin happened to have the real value and it looked good.
Tritium data (and uncertainty) plus flags are final and public
Expocode: 325020060213 Ship: Thompson Woce Line: P16 (2006) Note: Tritium data (and uncertainty) plus flags are final and public
Tritium data (and uncertainty) plus flags are final and public
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
helium/neon data
Expocode: 325020060213 Ship: THOMAS G THOMPSON Woce Line: P16 Note: From Bills' email message: "Please find attached the helium/neon data from the 2006 P16 reoccupation (expo code325020060213). Please let me know if you have any questions. Also, could you let me know if you have a copy of the tritium data for that cruise? I'm not sure whether/when that was submitted."
File CCHDO-2011-09-06.txt containing Trace Metals data,
submitted by Chris Measures on 2011-12-19, available under 'Files as
received', unprocessed by CCHDO.
Trace Metals data
Expocode: 325020060213 Ship: THOMAS G. THOMPSON/USA Woce Line: P16N Note: None
Thank you very much for your data submission to the CCHDO. Your file
P16N_Hg_bottle_file.xls submitted on 2011-10-13 is now available
online under 'Updates'. The data are currently online in 'as received' condition. We will
notify you once the data are merged into our standard formats and are
placed in the normal data area.
Mercury data with quality flags UMEHG, UTHG, FMHG, FTHG
Expocode: 325020060213 Ship: Thompson Woce Line: P16N Note: Mercury data resubmitted via email from David Krabbenhoft to Susan Piercy with station, cast and bottle information as well as added quality flags. David Krabbenhoft <dpkrabbe@usgs.gov>
Mercury data resubmitted via email from David Krabbenhoft to Susan Piercy with station, cast and bottle information as well as added quality flags.
2011-03-25
ALKALI data submitted by Alex Kozyr on 2011-03-16
- Merged ALKALI and ALKALI_FLAG_W with no issues.
- Converted to woce and netcdf formats.
- Checked over everything with the bottle compare tool
- Opened the exchange and woce files in JOA with no issues
ALKALI
New flag values for ALKALI
Expocode: 325020060213 Ship: Thomas G. Thompson Woce Line: P16N_2006 Note: Please, replace the ALKALI data with these new parameters, as we changed some quality flags in the file. Please, let me know when you post the new data file online. Thank you, Alex Kozyr
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.
Could you please change two (2) flags from 2 to 3 in the data set for P16N_2006 as
follows:
Sta-cast-bottle
pH
40-1-13
Alk
14-1-32
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.
The DOC and TDN final data from Dennis Hansell (RSMAS). Please, merge the data
Expocode: 325020060213 Ship: R/V Thomas Thompson Woce Line: P16N 2006 Note: The DOC and TDN final data from Dennis Hansell (RSMAS). Please, merge the data.
The DOC and TDN final data from Dennis Hansell (RSMAS). Please, merge the data.
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.
CDOM data submitted by Norm Nelson on 2008-06-18.
-I first ran this translate command on the file: tr '\r' '\n'
-Changed data from tab delimited to csv. Translated
CDOM names and quality flags to match our parameter list.
- For station 55 the bottle file has CAST=2 for all values.
The merge file had CAST=1. I changed this to CAST=2 for all
station 55 values.
This was also true for the following stations
STNNBR 1 CAST 1 -> 2
STNNBR 2 CAST 1 -> 2
STNNBR 7 CAST 1 -> 2
STNNBR 12 CAST 1 -> 2
STNNBR 21 CAST 1 -> 2
STNNBR 24 CAST 1 -> 2
STNNBR 29 CAST 1 -> 2
STNNBR 31 CAST 1 -> 2
STNNBR 34 CAST 1 -> 2
STNNBR 36 CAST 1 -> 3
STNNBR 45 CAST 1 -> 3
STNNBR 47 CAST 1 -> 2
STNNBR 55 CAST 1 -> 2
STNNBR 60 CAST 1 -> 2
The following parameters were merged:
CDOM325,CDOM325_FLAG_W,CDOM340,CDOM340_FLAG_W,CDOM380,CDOM380_FLAG_W,
CDOM412,CDOM412_FLAG_W,CDOMSL,CDOMSL_FLAG_W,CDOMSN,CDOMSN_FLAG_W
BrdU data was submitted by Craig Carlson on 2007-11-16.
I converted this file to csv by hand. The last column
was not labeled. It followed the BrdU column, and had
values that looked like flags, so I named it BRDU_FLAG_W.
The following parameters were merged:
BrdU,BrdU_FLAG_W
DCNS data was submitted by Craig Carlson on 2007-11-15.
I converted this file to csv with a ruby script. I noticed
that Dr. Carlson has the parameter 'Arabinose' as opposed
to our spelling of 'Arabanose'. The following parameters
were merged:
FUCO,FUCO_FLAG_W,RHAM,RHAM_FLAG_W,ARABA,ARABA_FLAG_W,
GALA,GALA_FLAG_W,GLUC,GLUC_FLAG_W,MAN,MAN_FLAG_W,DCNS
C13 and C14 data were submitted by Bob Key on 2008-04-07.
I changed a few parameter names in the header to match
the cchdo parameter list. The following parameters were
merged:
DELC14,C14ERR,DELC14_FLAG_W,DELC13,DELC13_FLAG_W
Carbon data was submitted by Alex Kozyr on 2007-10-19.
I changed the PH column header to be PH_TOT. Following
Alex's suggestion in his submission note, I deleted PCO2 and
PCO2_TMP.
merged:
TCARBN,TCARBN_FLAG_W,ALKALI,ALKALI_FLAG_W,FCO2,FCO2_TMP,
FCO2_FLAG_W,PH_TOT,PH_TEMP,PH_TOT_FLAG_W,DOC,DOC_FLAG_W
C13
Bob Key sent out an email on April 4th, 2009 asking that
this data not be merged until he submits a newer version.
Since I already merged the column into the data file,
I decided to mask their values, rather than remove them,
until we recieve the new data from Bob Key.
These data are beam attenuation numbers
Expocode: None Ship: None Woce Line: p16n Note: this appears to be a duplicate submission of the previously submitted p16n beam attenuation coefficients
Expocode: None Ship: None Woce Line: p16n Note: None
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.
Mercury data
Expocode: P16N 2006 Ship: Rv Thompson Woce Line: None Note: None
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.
Expocode: 325020060213 Ship: Thomas G. Thompson Woce Line: P16N Note: Replaces previously submitted data based on updated instrument calibration.
This data was merged, but there are issues with the C13 data. The C13 column is masked in the exchange bottle file.
Expocode: 325020060213 Ship: THOMAS G. THOMPSON Woce Line: P16N Note: None
Mary Johnson pointed out that the txt document for this cruise was one line, and contained unprintable characters. This has now been corrected.
Please see the attached files for our P16N underway data of pH, fCO2, and TCO2 and the data report. We are sorry for the delay. I've also included a note in the Excel file to explain each column. Blank fields are missing data due to bad measurements, but I did not put a flag number in it.
Expocode: 325020060213 Ship: Thompson Woce Line: P16N Note: These data are Bacterial Production data as measure by bromodioxyuridine (BrdU) incorporation. These data are ancillary to the core CDOM data set already submitted.
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.
Expocode: 325020060213 Ship: Thompson Woce Line: P16N Note: These are dissoved combined neutral sugar data that are ancillary to the core CDOM data (already submitted). Due to limited resources shore based analyses of DCNS samples for this cruise were focused on the 200- 300m depth horizon to address specific CDOM questions.
DCNS data.txt Type: Status: public
Name: Carlson, Craig
Institute: UCSB
Country: USA
Expo:325020060213 Line: P16N
Date: 2006-02-01
Action:Merge Data
Notes:These are dissoved combined neutral sugar data that are ancillary to the core CDOM data (already submitted). Due to limited resources shore based analyses of DCNS samples for this cruise were focused on the 200- 300m depth horizon to address specific CDOM questions.
Expocode: 325020060213 Ship: THOMAS G. THOMPSON Woce Line: P16N_2006 Note: 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. Please, let me know when these data will be merge and available online. Thanks, Alex.
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.
A new .csv bottle file for p16n_2006a (32502006021) is now online. It is the most
current .csv bottle file created from the merged data set of all final parameters submitted
to date for this cruise. Please take a look or just read and comment if necessary:
-It has the citation information (info used from Susan's file [obtained from Chris Sabine?])
trying to follow as best I could, Jerry's format using the condensed PI list.
-Our conversion code did not accept all the variations of pH values due to the unconventional
header mnemonics. Therefore pH values are not currently in the .csv file. This needs to
be noted. However, they are all contained within the WOCE formatted bottle file online.
When we hear back from either Bob Key or Alex Kozyr regarding the definitive measurements
to be used, I will regenerate the file to include just one pH value with the appropriate header.
-The code also did not convert PCO2@20, but did convert PCO2 and PCO2TMP. If this needs
to be changed to the former, please let me know and I will make those changes with the pH's.
I thought Bob and Alex slightly disagreed on this issue, however our code only complies
with the situation described above (unless header mnemonics are altered prior to
conversion).
Please just let me know if there are any problems with this, otherwise I'll finish it with
regard to pH's once we have word from CDIAC.
Dr. Feely asked me to submit the pH data from 2006 P16N cruise. I am
sorry it got delayed as I do not know the procedure. Attached please
find our pH data (last two column with data and qualifier). A simple
cruise data report was also attached. Bob may have some wording on the
cruise report but I do not want to delay the pH data further.
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.
These are the parameters that are NOT going to be included
in the .csv and subsequent netcdf files for P16N 325020060213:
The following columns are not going to be included:
----------------------------------------------------
CFC-113
CFC-113_FLAG_W
DOC
PCO2_20
PCO2_T
PH_UM
PH_UM_FLAG_W
PH_UM_T
PH_USFPH_USF_T
PH_USFPH_USF_T_FLAG_W
----------------------------------------------------
Writing data to file...
The exchange file was successfuly created: P16N_hy1.csv
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
File: P16 Final Data-v1.csv Type: ascii, comma separated Status: Public
Name: Mordy, Calvin
Institute: U of Washington/JISAO
Country: USA
Expo: 3250200602 Line: P16N
Date: 02/2006
Action:Place Data Online
Notes:
Upload directory: /incoming_data/20070302.110809_P16N_Mordy,_Calvin
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.
Attached is the nutrient data from the P16N2006 cruise. Please accept my apologies for the lateness of this submittal. The sample number is a combination of cast number and niskin number. For example 234 would be cast 2 and niskin 34.
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.
Lets just do a simple thing. Please delete all carbon files I've sent you before and use attached to this email file. It consists of TCARBN, ALKALI, PCO2_20, PH, DOC, and their flags.
All the data and flags are final and public. Please confirm that you received this file OK. And let me know when all data will be merged. I hope that Chris and Dick will help you to resolve all problems with hydrographic data.
In October 2006 Kristy McTaggart and I finalized the CTD and bottle salt files for P16N. At that time Kristy sent CCHDO final CTD files as well as updated bottle files with final CTD te,pr,sa, & O2, as well final flags for bottle sa. At the same time she sent some suggested flags for bottle O2 to Chris Langdon, the PI for that measurement. Steve Diggs at CCHDO acknowledged receipt of those file she sent to CCHDO. Kristy is following up on this with Danie to make sure that CCHDO has the finalized physical data. Kristy and I have done nothing with nuts or carbon parameters.
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>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.
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 file
or 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 as possible.
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).
I've talked with Alex regarding this issue, and he had no knowledge of any bottle file problems or any idea as to if he even had the most updated bottle file. We had a dead correspondence regarding any updates and no indication that you had forwarded a recalibrated file to Alex. It would help us tremendously if in the future you could update the file with us, then we would be on the same page as Alex (who often gets
bottle files from us to merge his data into) and be able to keep our online meta-data files as current as possible for any users who might be waiting for data to appear online.
Thanks again for the info and speedy reply. I will get back with Alex regarding this cruise and contact you if we need anything further.
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.
Regarding the samples from P16N, we are planning on starting the helium analyses early next year, so they should be finished by May or June, 2007. We are just now degassing the tritium samples, which means that due to storage requirements, they won't be ready for analysis until autumn, 2007.
Hi Steve,
I have just submitted the final DOC data measured during P16N-2006 cruise. I forgot to make a note, that some quality flags were changed from the original file that we received from Dennis. In case he sent his data to CCHDO as well, please use the the data I've submitted today.
Please, let me know when the DOC data will be merged with all hydrographic data at CCHDO.
Thank you,
Alex.
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:
Here are the latest update on the Carbon Data status at CCHDO and CDIAC.
P16N_2006:
TCO2 - OK;
TALK - not a final data merged in CCHDO files (data were sent to CCHDO on 8/28/2006);
pH - no pH data merged in CCHDO files (data were sent to CCHDO on 8/28/2006);
pCO2_20 - OK (only pCO2_20 and pCO2_20 FLAGS were reported, pCO2 and pCO2_TEMP columns should be deleted from the files at CCHDO).
DOC - no final data from Hansell.
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 have talked to Dennis yesterday. The DOC measurements are performed onshore and it takes longer time to finalize these data than other measurements made at sea. Dennis is in UK at this time, he will be back in two weeks. The data will be submitted to CDIAC shortly after his return.
I do anticipate a final update to the CFC data. I suspect it will be completed in mid-October.
The August 2nd files are the final ones. After I sent the data to CCHDO on Aug. 1, Bob Key from Princeton, who is my collaborator on QA-QC independent work sent me some additional quality flags which I incorporated in the final data files. All PIs have "finalized" the carbon data (pH, TALK, TCO2 and pCO2 parameters for P16N_2006 and TCO2 only for P16S_2005). The final data for P16N_2006 are open through CDIAC web page now and you could extract these parameters from the file to avoid any confusion. You can copy the final files at: http://cdiac.ornl.gov/oceans/RepeatSections/clivar_p16n.html and click on "Data files".
We made some corrections to the data files I've sent you yesterday (P16N_2006 and P16S_2005). The new files are attached. Please, discard both yesterday's files.
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.
I've just uploaded final DIC data and QC Flags to the web site: http://cchdo.ucsd.edu/ .
I did this for Dr's Feely and Sabine. They were uploaded as separate csv files. Please let me know if there are problems and/or questions.
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/>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.
Subject: Re: P16N DIC TALK and pH data
All of our quality control of the data is finished and we have complete our data report on the cruise. I am off on a trip tomorrow for a week and will have my group send you our final results next week.
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.
You have made an excellent suggestion. Let's go forward with that approach. Unfortunately, I do not have someone in my group to reformat that particular file format. Dan Greeley from my group is actively working on the DIC data this week and I will contact Frank Millero to see where he stands with the pH data.
Susan Piercy wrote:
Hi Dick,
From the recent email you sent to Lynne, it sounds like all bottle data except DIC and pH data should go online. Just want to make sure about this and ask for your formal permission.
If we have your permission to link all data except for these two parameters, can someone in your group reformat the file?
Please let me know.
Regards, Susan
Chris Sabine instructed me to send my preliminary data from the P16N cruise to you. This data was collected by myself, Sara Bender. It will be used by Paul Falkowski (Rutgers University). Chris said the data is classified as "level 3 measurements." I have attached an excel file as well as a brief description of what these measurements will be used for.
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.
I have received the final discrete pCO2 measurements from Rik Wanninkhof for P16N_2006 cruise (the World record for the final data submission). Could you please send me the preliminary bottle data files (both WOCE and Exchange format if it is possible), so I could merge the pCO2 data and other carbon-related data before I submit these data to CCHDO?
Thanks for doing this. There are some serious calibration problems with the bottle data that should be resolved before they are placed on the public website. Also the pH and discrete pCO2 data must be individually corrected for input and output temperatures before they placed on the website. We should not be placing incorrect or undocumented data on the website just to me meet a nominal
deadline.
Please call me before you place any of the P16N bottle data on the CCHDO website. I am certain that most the PIs, including myself, feel that this data is much too preliminary to be put on a public website at this time. In most cases, the data must be further corrected for standards, temperature corrections, etc, before we want the data on the website. I would prefer that you remove it immediately until we resolve this issue.
Also you should correct the website to have Sabine/Feely as co-chief scientists for the P16N cruise. There were two legs of this cruise and each of us was responsible for one of the legs. Chris and I have sent Jim copies of the individual cruise reports and they should be included in the documentation as pdf files.
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.
Attached please find a copy of our cruise report for P16N Leg 2 on the Thomas G. Thompson. Please post this cruise report on the cruise website. I will have Dana Greeley post it on the PMEL cruise website as well. Let me know if there are any other places that we should send it to.
I have attached the SEA, SUM, and WOCE EXCHANGE format data from the cruise. I can also send you the CTD data, but that is a bit large to send over email. Hopefully this is enough to get the site started, then when Frank returns in a couple of weeks he can give you the larger files.
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.