Hi all,
I am trying to harmonise taxonomic information in a dataset from a biodiversity study. So far I've tried several functions within the taxize package in RStudio.
I was referring to Grenié et al. (2022) (Article Harmonizing taxon names in biodiversity data: A review of to...
)for best practices and got the impression that the R package taxize is one of the most reliable tools for this task.However, many users report issues with this approach where repositories (e.g. Encyclopedia of Life) have suspended or limited their support for these services, rendering them unusable.
Hence my question: what R packages and online repositories do folks prefer to use to harmonise taxonomic data?
I appreciate your time to read my question and am grateful for any help you may provide.
All the best,
Giulio
I have recently been using taxize and myTAI combined via NCBI and have had no issues with it. Of course, you need to pre-process the data a bit to get rid of format issues. Keep in mind that it also depends on the organisms groups in question, e.g., plants are more complete than insects.
We used a custom-made R wrapper of taxize and rgbif (https://github.com/pozsgaig/CaraFun/blob/main/Data_cleaning/function_checkSpecies.R) for finding GBIF IDs and taxonomy for old taxon names for our Carabidae - Fungus association paper.