auxiliary variables plot

[RobFryer]

Issue #409
plot_assessment now also plots the raw data with key auxiliary variables. This is achieved by 'file_type = "auxiliary". The default variables are:

• biota: concentration, LNMEA, DRYWT%, LIPIDWT%
• sediment: non-normalised concentration, normalised concentration, AL, CORG
• water: no plots are currently produced

The choice of auxiliary variables can be altered using the auxiliary argument, although the options here are still limited.

Tested with the HELCOM and AMAP data.
Documentation updated.
AMAP vignette (which demonstrates plot_assessment) updated.

To close off this issue, still need to:

• update multi-series plots
• update ratio plots
• reintroduce these plots into the html reports for each time series
• remove warning about the distribution of MNC data

[RobFryer]

@annelaerkes @hallareinert
One of the checks has failed - I'll look at this over the next couple of days, update code, and let you know when done.

[RobFryer]

@annelaerkes @hallareinert
I renamed a couple of internal plotting functions, but forgot that they are called explicitly in the markdown. Have corrected this and the checks now work. Please can one of you review and, if happy, merge.

[annelaerkes]

This is an exiting addition. My only comment is on the explanatory text:

"At present, it is only possible to change the last three variable for biota and the last two variables for sediment. For example, for metals in sediment, you might specify auxiliary = c("AL", "LI") to plot aluminium and lithium concentrations instead of aluminium and organic carbon."

To me this description is unclear. Am I understanding it correct, that only the auxiliary variables can be changed, not the contaminants? If so, can we write that instead of the reference to "last two/three"?

[RobFryer]

@annelaerkes
I agree - it wasn't clear. I've had another go and hopefully it is better this time round. Still a bit convoluted though!

[annelaerkes]

I think this explanation is better, thanks