Description Usage Arguments Details Examples
Build a lookup table for a set of species, connecting the species names to plant genera, families and orders
1 2 3 | lookup_table(species_list, lookup_table = NULL, genus_column = "genus",
missing_action = c("drop", "NA", "error"), by_species = FALSE,
family.tax = "apweb", include_counts = FALSE, ...)
|
species_list |
Character vector of species bionomials Genus and species may be seperated by " " or "_" |
lookup_table |
Any higher taxonomy lookup table, but by default |
genus_column |
The column within |
missing_action |
How to behave when there are genera in the
|
by_species |
If |
family.tax |
There are two available family taxonomies–"apweb" and "plantlist". the default is "apweb" |
include_counts |
This will include the number of species in the genus (data from the plant list) in the output |
... |
variables passed on to |
The data within this lookup table comes from two sources:
1. The Plant List v1.1. (http://www.theplantlist.org/) for accepted genera to families and species richness within each genera. Note that we do not consider hybrids (e.g. Genus X species) as distinct species for this count while the plant list summary statistics do, so the the counts from this package will not line up exactly with the ones on the TPL website.
2. APWeb (http://www.mobot.org/MOBOT/research/APweb/) for family-level synonymies and family-to-order for all vascular plant families. Note that there is not currently order-level information available for Bryophytes.
1 2 3 4 5 6 7 8 9 10 11 12 | lookup_table("Pinus_ponderosa")
#
# or with a space
#
lookup_table("Pinus ponderosa")
#
#
# control how you want the function to handle non-matches
#
lookup_table(c("Pinus ponderosa","Neitheragenus noraspecies"))
#
lookup_table(c("Pinus ponderosa","Neitheragenus noraspecies"),missing_action="NA")
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