compile_taxa function returning unexpected classifications

[kdburke]

Using a pollen object returned by 'get_download,' I'm trying to use the 'WS64' list name as a first pass subset. It looks like some of the expected classifications are missing in the output, however:

• Expecting 'Fraxinus nigra,' 'Fraxinus pennsylvanica/americana' and 'Fraxinus undiff.' the output generated has 'Fraxinus' and 'Total.Fraxinus..sum.of.nigra.penn.undiff'
• Expecting 'Pinus diploxylon,' Pinus haploxylon,' Pinus undiff.,' and 'Pinus Southeast' the output is missing 'Pinus Southeast'
• 'Iva' is missing from the output
• 'Lycopodium' is missing from the output
• There is an additional classification called 'x.counts.good_counts...'

Looking at the original pollen object using 'compile_downloads' I can see the original classifications, so there should be Iva and Lycopodium in the output.

This same error can be reproduced by loading the attached Rdata file and running: sample_data_download.zip

test_dl_ws <- compile_taxa(test_dl, list.name = 'WS64', cf=TRUE, type=TRUE)

You can see in the column names there, the unexpected classifications, and missing 'Iva,' which is in the original taxa list for example. I've tried looking in the Neotoma repository at the compile_taxa.R code, but cannot find the classification lists to debug further myself.

Thank you in advance for any help/insight provided.