From: Annette DesRochers - NOAA Affiliate <annette.desrochers@noaa.gov>
Date: Thu, Jun 28, 2018 at 10:31 PM
Subject: coral demographic accessions, presence code lists
To: Zachary Mason - NOAA Affiliate <zachary.t.mason@noaa.gov>
Cc: Kevin Trick <kevin.trick@noaa.gov>, Brittany Huntington - NOAA Affiliate <brittany.huntington@noaa.gov>


Heya Zach

I looked into your question about the coral demographics presence codes and spoke with Dione, our corals person, to be sure I have all this straight. See your question and my response below.

Question: The coral demographics accessions for the Pacific Basin seem to be missing some supporting documentation. No, they are not missing any documentation. It looks like the presence codes files that were submitted before 2017 are vastly different from the ones submitted in 2017. No, presence code files have not been submitted in 2017; however, presence data files have been submitted, and this presence data used to be included in the observation data file, which is why a presence code file was required. Should I have 2017 files that look like the ones in the older submissions? No, you should not. I explain in further detail below.

In summary, a coral demographic accession for one NCRMP survey year should include:

Data
V0_CORAL_OBS_E_<REGION>_<YYYY>.csv
V0_CORAL_OBS_E_PRESENCE_<REGION>_<YYYY>.csv 
V0_CORAL_OBS_F_<REGION>_<YYYY>.csv 
<REGION><YYYY>_CoralGenera.csv
<REGION><YYYY>_CoralSpecies.csv 
Documentation
InPort.xml
iso19115.xml
Presence code files (different from the presence data files) are no longer used and are no longer needed since the observation data for all NCRMP years (2013-2017) have been updated to separate the observation data (V0_CORAL_OBS_E) from the presence/absence data (V0_CORAL_OBS_E_PRESENCE), and I believe all the coral data have been resubmitted and the corresponding accessions have been updated. On all of the accession pages, the Presence Code links should be removed from the documentation tab. 

All five data files (OBS E, OBS F, OBS E Presence, and the coral genera and species lists) should be included with the data accession (not the NCRMP documents accession) as the genera and species lists correspond directly to the surveys for that place and year. If a user navigates to the download links (HTTPS or FTP) to grab the data, they should be able to grab the code lists for genera and species with the data. Additionally the lists could be added to the documents accession as a copy, but if the lists need to be associated with one or the other accession, they should be archived with the data accession. I know this differs from what we discussed and from how most of the accessions are currently arranged, but having talked with Dione she felt pretty strongly about it, and now that I better understand all of this I agree with her. 

I went through each accession and listed the updates that are needed. Please make the changes below. 

Marianas 2014: 0159166  redirect the coral list links on the documentation page to point to the data accession, remove presence link, FTP does not include the files
Marianas 2017: 0166383   remove presence link (which is not correct)

PRIA 2014: 0159162   redirect the coral list links on the documentation page to point to the data accession, remove presence link, FTP does not include the files
PRIA 2015: 0159161   redirect the coral list links on the documentation page to point to the data accession, remove presence link, FTP does not include the files
PRIA 2016: 0159164  It doesn't look like coral genera and species lists were provided. Dione said the lists are the same as PRIA 2015 
PRIA 2017: 0163743  redirect the coral list links on the documentation page to point to the data accession

Am Samoa 2015: 0159173  redirect the coral list links on the documentation page to point to the data accession, remove presence link, FTP does not include the files        
Am Samoa 2016: 0159167   redirect the coral list links on the documentation page to point to the data accession, FTP does not include the files   

Hawaii 2013: 0159147  redirect the coral list links on the documentation page to point to the data accession, remove presence link, FTP does not include the files
Hawaii 2016: 0159163   redirect the coral list links on the documentation page to point to the data accession, remove presence link, FTP does not include the files (the coral lists are currently the same as 2013, however, Dione said this is a mistake. A 2016 list needs to be provided (there was one species change). Dione will send to me by COB tomorrow.

Many thanks for your patience - it took me some time to dig into this and to fully understand all the pieces and changes. Let me know if it'd be helpful to further discuss.

Annette
