Manage species groups in biomonitoR

Sometimes happens to have species groups in your data (e.g Rhyacophila nubila/obliterata). To overcome this issue you can import your data and putting the problematic species in the user’ custom database (and of course in the Taxa column of the database to analyse). Then you have to move to R where you must replace the slash (as in our example) with a space from both the database to analyse and from the custom database. This should assure that your species groups will be recognised by asBiomonitor.

 


# use gsub to replace slash with space 
# (macro is the database to analyze and user_db 
# the custom database to add to the reference database)
# for example we want to change species groups like
# Rhyacophila nubila/obliterata to Rhyacophila nubila obliterata

macro$Taxa <- gsub("/", "_", macro$Taxa, fixed = T)
user_db$Taxa <- gsub("/", "_", user_Db$Taxa, fixed = T)
user_db$Species <- gsub("/", "_", user_db$Species, fixed = T)

macro.asb <- asBiomonitor(macro, dfref = user_db, overwrite = F)

 

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