vignette for parsing and filtering biotic data

[edvinf]

Users have requested a vignette introducing how to use RstoxData to handle NMDbiotic-data in R-scripts.

The vignette should be IMR-centric and introduce how to get data from NMDbiotic and how to utilize any other resources such as the cruise database or bioticexplorer.

Important topics:

• fast reading with RstoxData::readXmlFile or RstoxData::ReadBiotic
• filtering of hierarchical data with RstoxData::FilterBiotic
• merging with RstoxData::mergeByIntersect
• handling of difficult merges (agedetermination). Perhaps just fix #282 in the same go.
• Link to authorative format documentation.

Other important topics to include:

• difference between cruise data and commercial samples
• the snapshop system in NMDbiotic
• different versions of biotic

[brianstock]

To include: easy way to get a list of cruise codes or serial numbers corresponding to a dataset/survey, e.g. for the coastal survey (https://datasetexplorer.hi.no/apps/datasetexplorer/v2/navigation/Cruiseseries/23). Elsewhere (Yves' code here, also here) I have seen Rstox::getNMDinfo for this:

Rstox::getNMDinfo(c("cs", "Varanger Stad NOR coastal cruise in autumn"))

I get the error:

Error in rbind(deparse.level, ...) : 
  numbers of columns of arguments do not match

This works at least:

Rstox::getNMDinfo("cs", recursive=F)[21]
[1] "Varanger Stad NOR coastal cruise in autumn"

Possibly because Rstox has not been updated in several years and never with R 4+. Is there another function for this?

Similar for the reference fleet, e.g. https://datasetexplorer.hi.no/apps/datasetexplorer/v2/navigation/Commercial%20sampling/Referansefl%C3%A5ten-Kyst. Currently using serial number range.

[edvinf]

Thanks. You are correct that API access has not been included in the new stox packages. I will include instructions for how to fetch data by cruise or sampling program in the vignette