Package 'FloraIberica'

Taxa distributions

Description

Taxa distributions

Usage

Distributions

Format

Distributions

A data frame with 1,824,549 rows and 6 columns:

Genus

genus

Species

species

Subspecies

subspecies

UTM.cell

Name of the 10x10 km UTM.cell

lng

longitude in decimal degrees

lat

latitude in decimal degrees

Source

https://doi.org/10.1111/geb.13363

---

Get a zonal checklist

Description

Get a checklist of the vascular plants growing near a given point or polygon.

Usage

get_checklist(zone = NULL, sf = FALSE)

Arguments

zone	A vector of two numbers giving the point longitude and latitude (in that order), an sf object with a single point coordinate, or a polygon sf object.
sf	Logical. If FALSE (default) return a dataframe with the checklist. If TRUE, return an sf object with the coordinates where each taxa is found. Note these point coordinates represent the centre of 10 km resolution UTM grid cells, not the actual location of these plants.

Value

A dataframe or sf object

Note

As the original data (AFLIBER database) have 10-km resolution, the resulting checklist may include taxa present within 10 km distance of the point or polygon.

Examples

sitio <- c(-5, 40)
head(get_checklist(sitio))

---

Get the distribution of one or more plant taxa

Description

Get the distribution of taxa on a 10 x 10 km UTM grid. Point coordinates represent the center of each grid cell, not actual plant locations.

Usage

get_distribution(genus = NULL, species = NULL, subspecies = NULL, sf = TRUE)

Arguments

genus	character. One or more genera to check for presence. Required, unless gbif.id is provided.
species	character. Optional. One or more species names to check for presence. The length of genus must equal that of species, unless length(genus) == 1, in which case it will be assumed that all species belong to that same genus.
subspecies	character. Optional. One or more subspecies names to check for presence. The length of species must equal that of subspecies, unless length(species) == 1, in which case it will be assumed that all subspecies belong to that same species.
sf	Logical. Return a spatial (sf) or a plain dataframe?

Value

An sf object if sf = TRUE, a plain dataframe otherwise.

Examples

abies <- get_distribution("Abies")
abies
unique(abies$Species)  # including all species in the genus

pinsapo <- get_distribution("Abies", "pinsapo")
pinsapo

---

Iberian Peninsula contour

Description

Iberian Peninsula contour

Usage

IberianPeninsula

Format

IberianPeninsula

A sfc_MULTIPOLYGON object with the contour of Portugal, Peninsular Spain and Balearic Islands

Source

https://www.naturalearthdata.com/

---

Is taxon endemic?

Description

Is taxon endemic of the Iberian Peninsula and/or Balearic Islands? That is, not present naturally elsewhere in the world.

Usage

is_endemic(genus = NULL, species = NULL, subspecies = NULL, gbif.id = NULL)

Arguments

genus	character. One or more genera to check for presence. Required, unless gbif.id is provided.
species	character. Optional. One or more species names to check for presence. The length of genus must equal that of species, unless length(genus) == 1, in which case it will be assumed that all species belong to that same genus.
subspecies	character. Optional. One or more subspecies names to check for presence. The length of species must equal that of subspecies, unless length(species) == 1, in which case it will be assumed that all subspecies belong to that same species.
gbif.id	character. Optional.

Details

For a genus to be considered endemic, all its species must be endemic. Likewise, for a species to be considered endemic, all its subspecies must be endemic.

Value

A logical vector

Examples

is_endemic("Laurus")
is_endemic("Aconitum")
is_endemic("Aconitum", "variegatum")
is_endemic("Aconitum", "napellus")
is_endemic("Aconitum", "napellus", c("vulgare", "castellanum", "lusitanicum"))

---

Is taxon present in the Iberian Peninsula and/or Balearic Islands?

Description

Is taxon present in the Iberian Peninsula and/or Balearic Islands?

Usage

is_present(genus = NULL, species = NULL, subspecies = NULL, gbif.id = NULL)

Arguments

genus	character. One or more genera to check for presence. Required, unless gbif.id is provided.
species	character. Optional. One or more species names to check for presence. The length of genus must equal that of species, unless length(genus) == 1, in which case it will be assumed that all species belong to that same genus.
subspecies	character. Optional. One or more subspecies names to check for presence. The length of species must equal that of subspecies, unless length(species) == 1, in which case it will be assumed that all subspecies belong to that same species.
gbif.id	character. Optional.

Value

A logical vector

Examples

is_present("Laurus")
is_present("Laurus", "nobilis")
is_present("Laurus", "azorica")
is_present("Laurus", c("nobilis", "azorica"))
is_present(gbif.id = "3034015")

---

Map taxa distributions

Description

Get a map with the distribution of one or more taxa. Must provide either an sf object (as returned by get_distribution()) or genus, species, subspecies...

Usage

map_distribution(
  distrib.sf = NULL,
  genus = NULL,
  species = NULL,
  subspecies = NULL,
  taxo.level = "species",
  facet = FALSE,
  colour = "medium sea green",
  include.name = TRUE,
  ...
)

Arguments

distrib.sf	An sf object as returned by get_distribution().
genus	character. One or more genera to check for presence. Required, unless gbif.id is provided.
species	character. Optional. One or more species names to check for presence. The length of genus must equal that of species, unless length(genus) == 1, in which case it will be assumed that all species belong to that same genus.
subspecies	character. Optional. One or more subspecies names to check for presence. The length of species must equal that of subspecies, unless length(species) == 1, in which case it will be assumed that all subspecies belong to that same species.
taxo.level	character Taxonomic level to show in the map. Either 'genus', 'species' (default) or 'subspecies'. If 'subspecies' argument is provided, taxo.level is automatically changed to 'subspecies'.
facet	Logical. For multiple taxa, make a single map with all taxa together, or make a multipanel (facetted) figure with one panel per taxa?
colour	character. When there is >1 taxon, only used if facet = TRUE.
include.name	Logical. When there is a single taxon to map, use taxon name as title?
...	Further params to be passed to ggplot2::facet_wrap() if facet = TRUE, or to ggplot2::geom_sf() if facet = FALSE.

Value

A map and ggplot2 object

Examples

laurus <- get_distribution("Laurus", "nobilis")
map_distribution(laurus)

map_distribution(genus = "Laurus", species = "nobilis")

abies <- get_distribution("Abies")
map_distribution(abies)
map_distribution(abies, facet = TRUE, ncol = 1)
map_distribution(abies, taxo.level = "genus")

# Map all the subspecies of a species
map_distribution(genus = "Berberis", species = "vulgaris", taxo.level = "subspecies")
map_distribution(genus = "Berberis", species = "vulgaris", subspecies = "seroi")

---

Plant taxa

Description

Plant taxa

Usage

Taxa

Format

Taxa

A data frame with 6,456 rows and 11 columns:

Taxon

Full taxon name

Scientific_Name

Scientific name

Endemic

Endemic in the Iberian Peninsula and/or Balearic Islands (TRUE/FALSE)

Genus

genus

Species

species

Subspecies

subspecies

Class

class

Order

order

Family

family

GBIF_id

GBIF unique ID for that taxon

POW_Name

Name of the taxon in Plants of the World database

Source

https://doi.org/10.1111/geb.13363

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