Append species information to RDBES data

[davidcurrie2001]

Users find it difficult to understand aphia ids but these are the only mandatory species information available in the RDBES. Can we append useful species information such as scientific name/common name to our RDBES data.

[KirstenBirchHaakansson]

I think it would be relativity simple to add scientific name, but not so straight forward with common name / FAO.

So a function for adding species information and as a start scientific name

[davidcurrie2001]

Related issues have been opened: #146 #147

[davidcurrie2001]

Example of adding scientific name to SA using the ICES Worms code list:

# Load some RDBES data
myObject <- createRDBESDataObject(input = "./tests/testthat/h1_v_1_19_18")
# Append ICES specWorms code list to SA data
# (the "Description" column contains the scientific name)
saWithSpecWorms <- dplyr::left_join(myObject[["SA"]],
                                    RDBEScore::icesSpecWoRMS,
                                    by=c("SAspeCode"="Key"))

[davidcurrie2001]

Example of adding scientific name to SA using the Aphia records from WoRMS:

# Load some RDBES data
myObject <- createRDBESDataObject(input = "./tests/testthat/h1_v_1_19_18")
aphiaRecords <- RDBEScore::wormsAphiaRecord
# Change the AphiaID to a char (so it is easier to join to the RDBES speCode field)
aphiaRecords$AphiaID <- as.character(aphiaRecords$AphiaID)
# Append ahpia records to SA data
# (the "scientificname" column contains the scientific name)
saWithAphiaID <- dplyr::left_join(myObject[["SA"]],
                                    aphiaRecords,
                                    by=c("SAspeCode"="AphiaID"))