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README.Rmd
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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# FloraIberica
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[](https://github.com/Pakillo/FloraIberica/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/Pakillo/FloraIberica?branch=master)
`r badger::badge_lifecycle("stable")`
`r badger::badge_repostatus("Active")`
[](https://hits.dwyl.com/Pakillo/FloraIberica)
[](https://hits.dwyl.com/Pakillo/FloraIberica)
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`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](https://doi.org/10.1111/geb.13363). This atlas provides the distribution of each taxon in a 10 x 10 km UTM grid.
## Installation
``` r
remotes::install_github("Pakillo/FloraIberica")
```
## Usage
```{r example}
library(FloraIberica)
```
### Checking if taxa are present in the Iberian Peninsula and/or Balearic Islands
```{r}
is_present(genus = "Laurus", species = c("nobilis", "azorica"))
```
### Checking if taxa are endemic
```{r}
is_endemic(genus = "Aconitum", species = "napellus",
subspecies = c("castellanum", "lusitanicum"))
```
### 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:
```{r}
get_distribution("Abies", "pinsapo")
```
### Making distribution maps
#### Single taxon
```{r laurus}
map_distribution(genus = "Laurus", species = "nobilis", size = 0.9)
```
#### Many taxa
Distribution of Iberian *Abies*:
```{r abies_together}
abies <- get_distribution("Abies")
map_distribution(abies)
```
You can also get one map per taxon (species):
```{r abies_facet}
map_distribution(abies, facet = TRUE, ncol = 1)
```
Or collapse all presences of the entire genus:
```{r abies_collapse}
map_distribution(abies, taxo.level = "genus", size = 0.9)
```
Another example with Iberian pines:
```{r pines, out.width="100%", fig.asp=1}
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](https://pakillo.github.io/FloraIberica/reference/get_checklist.html):
```{r}
site <- c(-5, 40)
head(get_checklist(site))
```
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):
```{r cache = TRUE}
cadiz <- mapSpain::esp_get_prov_siane("Cadiz", epsg = "4326")
head(get_checklist(cadiz))
```
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):
```{r cadiz.qpyr, message=FALSE, cache = TRUE}
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
```{r comment=NA}
citation("FloraIberica")
```
## 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).
