Remove duplicate CTD casts from RL SCS data

[jrenfree]

Duplicate button presses exist for CTD casts in the .elg files. Should be 7 casts. Remove button presses where Notes field is NA.

[jrenfree]

I know that this is an existing issue in the estimATM repository, but thought I'd make one here as well for easier tracking within the AST project.

[jrenfree]

@kstierhoff I'll plan to try and tackle this for now in a new estimATM branch.

[jrenfree]

Well the UCTD data doesn't contain GPS data, and it doesn't appear that anyone filled out the UCTD info in the electronic log book, so it looks like the SCS data might be our best bet.

Any other ideas?

[kstierhoff]

I actually instructed folks to not enter GPS data into the cast files. It's tedious and error prone, IMO. Maybe a good backup option. Instead, I merge the cast files with the nav data from ERDDAP. I think this is the time to create a subroutine for processing casts, and be used in various places (eg plotCTD, and elsewhere). This code is correctly duplicated and should be consolidated. Let's discuss how best to tackle it. I have some ideas.

[jrenfree]

Do you want to tackle that? It certainly seems like the code in plotCTD.Rmd can be reused, but reportSurvey should not be dependent on plotCTD being run first.

Perhaps either input the necessary parts directly into reportSurvey or create a separate script/function that gets called by both plotCTD and reportSurvey?

[kstierhoff]

Yes, I can tackle that. I plan to put the processing code from plotCTD into a subroutine that extracts nav data from ERDDAP or SCS for the time period in the cast files. It will be stand-alone. Sound good?

[jrenfree]

Sounds good. I'll go ahead and delete the branch I had created.

[jrenfree]

Kevin added some new scripts that get called by reportSurvey and plotCTD, which reads the (U)CTD headers and data.

[kstierhoff]

Kevin is the bestest.