Option to exclude legacy data and other dataQF tags

[claraqin]

There should be some code to allow the user to exclude legacy data and other dataQF tags from the sequence files they download.

In the Technical Working Group meeting on Oct. 5, we discussed doing this with a simple grep command to subset the metadata object. However, there is a planned revision to download files using zipsByURI, which only accepts metadata from a file location, so after this revision is made, slightly more code must be added in order to write the subsetted metadata to file.

I don't have a strong preference between creating a new function for this, versus just producing a few lines of code that we could put into the "Download NEON Data" vignette.

[lstanish]

@claraqin I'm leaning towards including a couple of lines of code in the vignette highlighting these decision points, given that there are numerous options and it's hard to code them all in a clean function. Some of the components to highlight could be:

• in the mmg_soilRawDataFiles table: dataQF=legacyData
• in the mmg_soilRawDataFiles table: records are run-level or sample level, based on value in rawDataFileDescription
• in the mmg_soilPcrAmplification.16S (or ITS) tables: filter to records with the same the forwardPrimer and reversePrimer values

Thoughts? Suggestions?

[lstanish]

@claraqin Just re-visiting this issue, and I like the idea of having the QC function check the F and R primers. Will add that to the list of QC checks in the QF function GH issue. Is it OK to close this issue?

[claraqin]

Yes, it is! Thanks for taking care of this.