# Retrieve the lowest common taxon and rank for a given taxon name or ID ```r lowest_common(...) ## Default S3 method: lowest_common( sci_id, db = NULL, rows = NA, class_list = NULL, low_rank = NULL, x = NULL, ... ) ## S3 method for class 'uid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'tsn' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'gbifid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ## S3 method for class 'tolid' lowest_common(sci_id, class_list = NULL, low_rank = NULL, ...) ``` ## Arguments - `...`: Other arguments passed to `get_tsn()`, `get_uid()`, `get_gbifid()`, `get_tolid()` - `sci_id`: Vector of taxa names (character) or id (character or numeric) to query. - `db`: character; database to query. either `ncbi`, `itis`, `gbif`, `tol`. If using ncbi, we recommend getting an API key; see taxize-authentication - `rows`: (numeric) Any number from 1 to infinity. If the default NA, all rows are considered. Note that this parameter is ignored if you pass in a taxonomic id of any of the acceptable classes: tsn, gbifid, tolid. NCBI has a method for this function but rows doesn't work. - `class_list`: (list) A list of classifications, as returned from `classification()` - `low_rank`: (character) taxonomic rank to return, of length 1 - `x`: Deprecated, see `sci_id` ## Returns NA when no match, or a data.frame with columns * name * rank * id ## Authentication See taxize-authentication for help on authentication ## Examples ```r ## Not run: id <- c("9031", "9823", "9606", "9470") id_class <- classification(id, db = 'ncbi') lowest_common(id[2:4], db = "ncbi") lowest_common(id[2:4], db = "ncbi", low_rank = 'class') lowest_common(id[2:4], db = "ncbi", low_rank = 'family') lowest_common(id[2:4], class_list = id_class) lowest_common(id[2:4], class_list = id_class, low_rank = 'class') lowest_common(id[2:4], class_list = id_class, low_rank = 'family') # TOL taxa <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea") (cls <- classification(taxa, db = "tol")) lowest_common(taxa, db = "tol", class_list = cls) lowest_common(get_tolid(taxa), class_list = cls) xx <- get_tolid(taxa) lowest_common(xx, class_list = cls) spp <- c("Sus scrofa", "Homo sapiens", "Nycticebus coucang") lowest_common(spp, db = "ncbi") lowest_common(get_uid(spp)) lowest_common(spp, db = "itis") lowest_common(get_tsn(spp)) gbifid <- c("2704179", "3119195") lowest_common(gbifid, db = "gbif") spp <- c("Poa annua", "Helianthus annuus") lowest_common(spp, db = "gbif") lowest_common(get_gbifid(spp)) cool_orchid <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea") orchid_ncbi <- get_uid(cool_orchid) orchid_gbif <- get_gbifid(cool_orchid) cool_orchids2 <- c("Domingoa haematochila", "Gymnadenia conopsea", "Masdevallia coccinea") orchid_itis <- get_tsn(cool_orchids2) orchid_hier_ncbi <- classification(orchid_ncbi, db = 'ncbi') orchid_hier_gbif <- classification(orchid_gbif, db = 'gbif') orchid_hier_itis <- classification(orchid_itis, db = 'itis') lowest_common(orchid_ncbi, low_rank = 'class') lowest_common(orchid_ncbi, class_list = orchid_hier_ncbi, low_rank = 'class') lowest_common(orchid_gbif, low_rank = 'class') lowest_common(orchid_gbif, orchid_hier_gbif, low_rank = 'class') lowest_common(get_uid(cool_orchid), low_rank = 'class') lowest_common(get_uid(cool_orchid), low_rank = 'family') lowest_common(orchid_ncbi, class_list = orchid_hier_ncbi, low_rank = 'subfamily') lowest_common(orchid_gbif, class_list = orchid_hier_gbif, low_rank = 'subfamily') lowest_common(orchid_itis, class_list = orchid_hier_itis, low_rank = 'class') ## Pass in sci. names nms <- c("Angraecum sesquipedale", "Dracula vampira", "Masdevallia coccinea") lowest_common(x = nms, db = "ncbi") lowest_common(x = nms, db = "gbif") ## End(Not run) ``` ## Author(s) Jimmy O'Donnell jodonnellbio@gmail.com Scott Chamberlain

lowest_common function