alternative_syns_vector: Produces alternative species names vector
In FranzKrah/rmycobank: Interface to mycobank.org

Description Usage Arguments Details Value Author(s) Examples

Take the output from search_syn_in_ncbi and produces and alternative species vector substituting the species not present on NCBI GenBank by synonyms that are present

1	alternative_syns_vector(search_syn_in_ncbi_out)

search_syn_in_ncbi_out

takes the output from search_syn_in_ncbi

This function is motivated as a helper for producing an input for MEGAPTERA. MEGAPTERA takes an input taxa dataset and automatically procecces downloaded sequences. However, it does not look for synonyms, which is a problem - especially for fungi. alternative_syns_vector, as the name says takes synonyms as input and produces a new vector of species names but subsitures "blind" species, thus species not present on GenBank but the synonyms are.

data.frame cols: facultative synonnmys, obligate synonyms and a combined new vector

Franz-Sebastian Krah

taxa <- c("Heterobasidion annosum","Schizopora paradoxa")
s <- search_syn_in_ncbi(taxa)
spec <- alternative_syns_vector(search_syn_in_ncbi_out = s)
spec$syns