FloraIberica

FloraIberica R package facilitates access to taxonomic and distribution data for the c. 6500 vascular plants present in the Iberian Peninsula and Balearic Islands, based on the AFLIBER database. This atlas provides the distribution of each taxon in a 10 x 10 km UTM grid.

Installation

remotes::install_github("Pakillo/FloraIberica")

Usage

library(FloraIberica)

Checking if taxa are present in the Iberian Peninsula and/or Balearic Islands

is_present(genus = "Laurus", species = c("nobilis", "azorica"))
#> Laurus nobilis Laurus azorica 
#>           TRUE          FALSE

Checking if taxa are endemic

is_endemic(genus = "Aconitum", species = "napellus", 
           subspecies = c("castellanum", "lusitanicum"))
#> Aconitum napellus castellanum Aconitum napellus lusitanicum 
#>                          TRUE                         FALSE

Getting the distribution of plant taxa

Returns sf or dataframe with the coordinates of the centre of 10 x 10 km UTM grid cells where taxa are present:

get_distribution("Abies", "pinsapo")
#> Simple feature collection with 30 features and 4 fields
#> Geometry type: POINT
#> Dimension:     XY
#> Bounding box:  xmin: -5.522 ymin: 36.438 xmax: -4.401 ymax: 36.991
#> Geodetic CRS:  WGS 84
#> First 10 features:
#>     Genus Species Subspecies UTM.cell              geometry
#> 213 Abies pinsapo       <NA>  30STF76 POINT (-5.519 36.704)
#> 214 Abies pinsapo       <NA>  30STF77 POINT (-5.522 36.794)
#> 215 Abies pinsapo       <NA>  30STF85 POINT (-5.404 36.616)
#> 216 Abies pinsapo       <NA>  30STF86 POINT (-5.407 36.706)
#> 217 Abies pinsapo       <NA>  30STF87  POINT (-5.41 36.796)
#> 218 Abies pinsapo       <NA>  30STF88 POINT (-5.413 36.887)
#> 219 Abies pinsapo       <NA>  30STF93 POINT (-5.287 36.438)
#> 220 Abies pinsapo       <NA>  30STF95 POINT (-5.292 36.619)
#> 221 Abies pinsapo       <NA>  30STF97 POINT (-5.298 36.799)
#> 222 Abies pinsapo       <NA>  30STF99 POINT (-5.303 36.979)

Making distribution maps

Single taxon

map_distribution(genus = "Laurus", species = "nobilis", size = 0.9)

Many taxa

Distribution of Iberian Abies:

abies <- get_distribution("Abies")
map_distribution(abies)

You can also get one map per taxon (species):

map_distribution(abies, facet = TRUE, ncol = 1)

Or collapse all presences of the entire genus:

map_distribution(abies, taxo.level = "genus", size = 0.9)

Another example with Iberian pines:

library(ggplot2)
map_distribution(genus = "Pinus", facet = TRUE, ncol = 2) + 
  theme(axis.text = element_text(size = 6))

Get a checklist of the plants present near a point or polygon

If you want to know the plants near a given site, just pass the coordinates to get_checklist:

site <- c(-5, 40)
head(get_checklist(site))
#>         Genus          Species     Subspecies
#> 1        Acer   monspessulanum monspessulanum
#> 2 Adenocarpus           aureus           <NA>
#> 4 Adenocarpus      complicatus           <NA>
#> 5      Allium scorzonerifolium           <NA>
#> 6       Alnus        glutinosa           <NA>
#> 7     Alyssum      fastigiatum           <NA>

The site can be a polygon, so you can easily obtain a list of the plants present within a given area (e.g. town, province, natural reserve):

cadiz <- mapSpain::esp_get_prov_siane("Cadiz", epsg = "4326")
head(get_checklist(cadiz))
#>       Genus        Species     Subspecies
#> 1     Abies        pinsapo           <NA>
#> 11     Acer monspessulanum monspessulanum
#> 21     Acer         opalus     granatense
#> 22   Aceras anthropophorum           <NA>
#> 33 Achillea       ageratum           <NA>
#> 57 Achillea        odorata           <NA>

You can also obtain an sf object rather than a dataframe, so you know where each plant occurs within or near that polygon (with a resolution of 10x10 km inherited from the AFLIBER database):

cadiz.qpyr <- get_checklist(cadiz, sf = TRUE) |> 
  dplyr::filter(Genus == "Quercus", Species == "pyrenaica")

ggplot() +
  geom_sf(data = cadiz) +
  geom_sf(data = cadiz.qpyr) +
  theme_bw()

Citation

citation("FloraIberica")
If you use FloraIberica, please cite both the data source and the
package as:

  Ramos-Gutiérrez I., Lima H., Pajarón S., Romero-Zarco C., Sáez L.,
  Pataro L., Molina-Venegas R., Rodríguez M. Á. & Moreno-Saiz J. C.
  (2021). Atlas of the vascular flora of the Iberian Peninsula
  biodiversity hotspot (AFLIBER). Global Ecology and Biogeography, 30,
  1951– 1957. https://doi.org/10.1111/geb.13363

  Rodríguez-Sánchez Francisco. 2023. FloraIberica: Taxonomic and
  distribution data for the vascular plants of the Iberian Peninsula
  and Balearic Islands. https://pakillo.github.io/FloraIberica

To see these entries in BibTeX format, use 'print(<citation>,
bibtex=TRUE)', 'toBibtex(.)', or set
'options(citation.bibtex.max=999)'.

Funding

The development of this software has been funded by Fondo Europeo de Desarrollo Regional (FEDER) and Consejería de Transformación Económica, Industria, Conocimiento y Universidades of Junta de Andalucía (proyecto US-1381388 led by Francisco Rodríguez Sánchez, Universidad de Sevilla).