I am trying to use the Metaboanalyst Compound Name/ID Standardization tool in the R package but am noticing that the results are different than when I run the same list of compound names through the web interface. The matching seems to be much worse using the R package. Is there a substantive difference in the codebase for the R package when using this tool compared to the API/Web version?
They are identifical - all the R functions used by web are directly pulled from the MetaboAnalystR GitHub. It should be something else.