species naming issues

[mikeallen-eco]

M. Karp pointed out several species naming issues and shared code that would help fix it. These are summarized below and the word file attached goes into greater detail. Also attached are a word file with proposed edits to the taxonomy file and an edited version of the compile.R code that illustrates how to fix some of these.

1. some species that are now filtered out of the final data due to lack of temporal coverage could be reinstated as a complex (e.g., Blackspotted and Rougheye rockfish);
2. some species that are currently listed as a complex may be better to split into their constituent species (Arrowtooth and Kamchatka flounder).
3. the "species" with common name "NA" and scientific name "NA" currently makes it through to the final data file.
4. Winter Flounder and Yellowtail Flounder may be currently deleted from the NEUS data set due to white space in the name (and resulting mismatch with taxonomy file); but this may have been fixed already.
5. Some species are missing common names (e.g., Geryon (Chaceon) quiquidens – Atlantic deep sea red crab is missing common name in Tax file).

Here is a more thorough description of the potential issues:
Species_data_issues (1).docx

Here are the proposed edits to the taxonomy file and code:
Changes to spptaxonomy (1).docx
compile_mkedits_1_27_22 (1).txt