get_species_: Get data from SPECIE framework

In edelcallejoc/rspecies: A Spatial Data Mining Framework for Species Distribution Modelling

Description

a family functions to extract data from SPECIES WEB framework.

Usage

get_species_names(level = "genus", name = NULL, sublevel, id = TRUE)

get_species_coords(species = NULL, from = "SPECIES", date = TRUE)

get_species_grid(grid_res = 16)

get_species_georel(target, start_level, value, grid_res = 16,
  validation = FALSE, fossil = TRUE, no_date = TRUE, min_occ = 1,
  bioclim = FALSE)

Arguments

level	a character vector of length 1. The name of the taxonomic rank. The allowed values are: "kingdom", "phylum", "class", "order", "family", "genus" and "specie". By default "genus".
name	a character vector of length 1. The name of the specie desired as web SPECIES platform shows.
sublevel	character or NULL. A vector of length 1. The name of taxonomic rank sublevel to search names. See examples.
id	Logical. If TRUE, id metada is included in the output. If FALSE only the names of species are display.
species	a character vector of length 1. The name of the specie desired as web SPECIES platform shows.
from	The name of web platform to consult data. At this point it only works for http://species.conabio.gob.mx.
date	logical. If TRUE the collection date is added.
grid_res	The resolution of the grid in km. The resolution at this momment are 8, 16, 32, and 64 km.
target	a character vector of length 1. The name of the specie desired as web SPECIES platform shows.
start_level	a character vector of length 1. The name of the taxonomic rank. The allowed values are: "kingdom", "phylum", "class", "order", "family", "genus" and "specie".
value	a character vector of length 1. The taxonomic name associated to the taxonomic rank (level argument) as web SPECIES platform shows.
validation	logical. If TRUE validation process is applied to the model.
fossil	logical. If TRUE fossil data is included in the model.
no_date	logical. If TRUE data without recolection date is included.
min_occ	numeric. The minimum number of cells occurrences (nj).
bioclim	logical. If TRUE bioclim data is included in the model.

Value

get_species_names() returns a data.frame object.

get_species_coords() returns a data.frame object.

get_species_grid() returns a SpatialPolygonsDataFrame object. It includes all the polygons that form the grid. Data slot contains the identifiers for each cells.

a data.frame object.

Note

get_species_names. The data can be very large so proceed with carefull.

get_species_coords. Only one species per query is allowed. This restriction is for memory care purposes. You can use the 'apply' function family to extend your search, but it is recommended to do the search one by one to not exceed the memory limits.

Author(s)

Enrique Del Callejo Canal ([e-mail]).

References

http://species.conabio.gob.mx/

Examples

# get_species_names() examples

# Initial capital letter
get_species_names(name = "Aedes")

# lowercase is allowed
get_species_names(name = "aedes")

# Cheking names of a level
# Cheking class' names of Craniata phylum
get_species_names(level = "phylum", name = "Chordata",
 sublevel = "class", id = FALSE)

# Cheking class' names of Animalia kingdom
get_species_names(level = "kingdom", name = "Animalia",
 sublevel = "class", id = FALSE)



library(httr)
library(jsonlite)

# get_species_coords() examples

# Lynx rufus

# Checking names

LR<-get_species_coords(species = "Lynx rufus")
LR

# Aedes aegypti
AA<-get_species_coords(species = "Aedes (Stegomyia) aegypti")
AA


# get_species_grid() examples

# By default resolution is 16 km.
system.time(a16 <- get_species_grid())

system.time(a32 <- get_species_grid(grid_res = 32))



Model1 <- get_species_georel(target = "Aedes (Stegomyia) albopictus",
    start_level = "class", value = "aves", min_occ = 5)

head(Model1)

edelcallejoc/rspecies documentation built on May 27, 2019, 7:25 a.m.