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Defunct functions in taxize

Source: R/taxize-package.R
taxize-defunct.Rd

The following functions are now defunct (no longer available):

  • All COL functions are defunct: as.colid, col_children, col_classification, col_downstream, col_search, get_colid, get_colid_, as.data.frame.colid, children.colid, classification.colid, downstream.colid, id2name.colid, lowest_common.colid, synonyms.colid, upstream.colid`

  • col_classification(): Seeclassification()

  • tp_classification(): Seeclassification()

  • eol_hierarchy(): Seeclassification()

  • eol_invasive(): See eol in the originr package.

  • use_eol(): EOL no longer requires an API key

  • tpl_search(): Use the Taxonstand functions TPL or TPLck directly.

  • get_seqs(): This function changed name toncbi_getbyname()()].

  • get_genes(): This function changed name toncbi_getbyid()()].

  • get_genes_avail(): This function changed name toncbi_search()()].

  • ncbi_getbyname(): See ncbi_byname in the traits package.

  • ncbi_getbyid(): See ncbi_byid in the traits package.

  • ncbi_search(): See ncbi_searcher in the traits package.

  • gisd_isinvasive(): See gisd in the originr package.

  • ubio_classification(): The uBio web services was down for quite a while, is now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.

  • ubio_classification_search(): The uBio web services was down for quite a while, is now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.

  • ubio_id(): The uBio web services was down for quite a while, is now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.

  • ubio_ping(): The uBio web services was down for quite a while, is now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.

  • ubio_search(): The uBio web services was down for quite a while, is now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.

  • ubio_synonyms(): The uBio web services was down for quite a while, is now (as of 2016-05-09) back up, but we don't trust that it will stay up and available.

  • get_ubioid(): The uBio web services are apparently down indefinitely.

  • phylomatic_tree(): This function is defunct. See phylomatic in the package brranching

  • phylomatic_format(): This function is defunct. See phylomatic_names in the package brranching

  • eubon(): This function is defunct. Use eubon_search()

  • tnrs(): This function is defunct. Was too unreliable

  • tnrs_sources(): This function is defunct. Was too unreliable