data(pollen.equiv) no longer works

[andydawson]

It used to be possible to view the pollen translation table using data(pollen.equiv). Not sure if the name of the table has changed, or if it no longer gets loaded properly when the package is loaded.

[davidfastovich]

Having the same issue as well

[davidfastovich]

Translation table only has 60 taxa in it for WS64 and below is why that happens:

The translation table sums together Fraxinus nigra and Fraxinus pennsylvanica/americana into Total Fraxinus for WS64 when they're all supposed to be separate. Iva is summed into Asteraceae when its also supposed to be separate. Southeast Pinus is also a taxa in the Williams and Shuman paper, but I'm not sure how this should be implemented considering the NAMPD has its own regional splits that accomplish this.

[SimonGoring]

I've added the translation table back into the package as its own data object.

These changes were pushed to the branch: https://github.com/SimonGoring/neotoma/tree/taxon_fixes

It will be merged with the main branch soon-ish, once I've made sure it passes all the neccessary tests.

For Fraxinus the issue is that there are sites with undifferentiated Fraxinus, and so taxa needed to be lumped to the lowest connom taxonomic unit. I believe that's the case with the other taxonomic groups. One solution for grographic bounds is to add a POLYGON column in the table, and to use that as well in assigning classes.

[davidfastovich]

Thanks for the quick fix, Simon! I built the package and data("pollen_equiv") works perfectly!

I might be confused, but in the paper the 64 species taxa list includes the more specific Fraxinus nigra and Fraxinus pennsylvanica/americana as separate from Total Fraxinus. I assumed this meant that where possible Fraxinus identifiable to the species level, if nigra (for instance), would be put into Fraxinus nigra, not Total Fraxinus.

Unrelated, but an actual typo: cf. Fraxinus in pollen.equiv[1896,] is Fraxinus for WS64 not Total Fraxinus (sum of nigra/penn/undiff).

[davidfastovich]

To clarify the Fraxinus thing, Total Fraxinus would then include Fraxinus that was not identifiable to the nigra, americana, or pennsylvanica species.