manual fixes once SRDB import is final

[teixeirak]

Running list:

• history/ plot name for Husnain_2014_ceft site "R-SF" (should be fixed in SRDB)
• stand age on Beyer_1991_icav
• cases where one of multiple plots at a site has age = NAC (likely duplicates with other plots). See issue SRDB import: count records with consecutive Study_midyear as single plot #183. List: sites_with_NAC_and_at_least_one_other_age
• cases where there are plots where its not clear whether similar ages are the same or different plots. See issue SRDB import: count records with consecutive Study_midyear as single plot #183. List: sites_legitimately_complicated
• review SRDB Notes field, make adjustments as needed. I added this document to identify and track the notes that need review. I started noting what needs to be done. Most should be very straightforward, but some may get a bit complex.
• there will be a lot of sites with stand.age=NAC. Review of these (some of which may be duplicates of existing sites/plots) could quickly result in more useable data. (@beckybanbury, looking these up-- or at least getting the papers-- is something you could work on before the merge is finalized, keeping a separate record (but note that some plot names will change, issue SRDB import cleanup #178 ).
• KAT: review D.precedence for records from Oishi_2013_satv
• review outliers
• merge duplicate sites

[beckybanbury]

There are a few instances where the species listed in veg.notes don't match with the dominant.veg classification. The description in the plot name often does match the dominant.veg classification, so we would have to decide if we want to override this or not @teixeirak @ValentineHerr . A running list of IDs in ForC to double check is:

• 26124 - 26134
• 26157 - 26167
• 28289
• 26901
• 25876 - 9
• 25465 - 8
• 21690 - 1

[beckybanbury]

@ValentineHerr @teixeirak I'm not clear from issue #183 how you want to deal with the differences in stand ages; Valentine, did you get any further with this at all?

In terms of correcting the notes, where are the "SRDB notes"? Is that in SRDB, or notes in the source.notes of ForC measurements?

[ValentineHerr]

I am working on issue 183

[teixeirak]

In terms of correcting the notes, where are the "SRDB notes"? Is that in SRDB, or notes in the source.notes of ForC measurements?

They are in SRDB. I have created this document to identify and track the notes that need review. I started noting what needs to be done.

[beckybanbury]

They are in SRDB. I have created this document to identify and track the notes that need review. I started noting what needs to be done.

So this is something that needs fixing in SRDB, not in ForC?

[teixeirak]

No, we need to go through the SRDB notes to capture relevant info that could not be dealt with by the automatic import. For example, notes about the geographic coordinates should go in a notes field in the SITES table, notes indicating different source for C variables other than respiration mean we should change the citation.ID in MEASUREMENTS, etc.

Does my document make sense now?

[ValentineHerr]

update on issue #181,
I have fixed most of the ages and plot names of the legitimately complicated sites.

This file keeps a record of old vs new plotnames.

I used this file to write down how things needed to be changed and as you can see there are a handfull of sites that need more investigation. I'll try to get to them soon.

I'll look into the cases where age = NAC

[ValentineHerr]

update on issue #181
I made some progress on some of the "age=NAC" issues but there is still a few that need investigation (see this file)
We are limited by online access of papers.
Also, in a lot of cases there is only one paper referenced for the site, so all ages (including age = NAC) come from the same paper, which makes me think that that paper must be mentioning a site of unknown age.

[teixeirak]

There are a few instances where the species listed in veg.notes don't match with the dominant.veg classification. The description in the plot name often does match the dominant.veg classification, so we would have to decide if we want to override this or not @teixeirak @ValentineHerr . A running list of IDs in ForC to double check is:

@beckybanbury , I've checked all of these and updated dominant.veg and plot names. We will need to rerun the plots script (+ others), but I'm still working on updates so won't do it now.
The numbers listed about that I did not tick off were ones with NAC in the veg description, or were missing, so I'm confused as to why they're there.

[teixeirak]

@ValentineHerr, I'm just realizing that I should have recorded plot name changes in this file. I have to go to a meeting now and probably won't have time to go back and do that today. My commits in the past hour or so included plot name changes.

Disregard. I have now added the plots.*

[teixeirak]

I have made some changes that will require re-running the duplicates code, ForC simplified, etc. There are still more manual fixes to be made, so probably no point in doing that now.