vignettes/get_species-vignette.md

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

SPECIES web platform is an interactive tool for the analysis of ecological niches and forecast species potential distribution, as well as to build Complex Inference Networks to identify potential species interactions. SPECIES development is supported by C3-Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México and the Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO).

This tutorial is a basic intriduction to use the r functions that connects to SPECIES api. This functions are contained in the developing package rspecies. rspecies is allocated in github public repositorie https://github.com/edelcallejoc/rspecies.

Vignette Info

The information contained in this vignette is corresponds to the usages of r functions to interact with SPECIES api. There are four functions that allows to extract information about SPECIES database's names. Each function can be used for many porpuses from consulting species names to adjust models in several ways.

Consulting taxon names from SPECIES framework (get_species_names)

The simplest way to use get_species_names is for cheking species names available for a specific taxon rank. For example, the names of the species of Aedes genus.

library(rspecies)

aedes <- get_species_names(level = "genus", name = "Aedes", id = FALSE)

head(aedes, n=5)
#                    name
# 1         Aedes aegypti
# 2      Aedes albopictus
# 3      Aedes allotecnon
# 4 Aedes angustivittatus
# 5  Aedes atactavittatus

A more complex example is to extract species' name from a higher taxon level. For example, The names of the species of Mammalia class.

mammal <- get_species_names(level = "class", name = "Mammalia", sublevel = "specie", id = FALSE)

head(mammal, n=5)
#                         name
# 1          Alouatta palliata
# 2           Alouatta villosa
# 3  Ammospermophilus harrisii
# 4 Ammospermophilus interpres
# 5  Ammospermophilus leucurus

It is important to declared id = FALSE in order to avoid extensive computation. The id argument is intended to be used for individual queries by species.

Extracting species' coordinates from SPECIES framework (get_species_coords)

The function get_species_coords is made to extract the geographical coordinates of observations by species from the API of the SPECIES framework. The simplest way to use this function is to indicate the species argument with the name of a particular species, eg Lynx rufus.

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

head(LR_coords, n=5)
#        Long      Lat    date       name
# 1 -100.0494 25.78639 1967-01 Lynx rufus
# 2 -100.0669 21.50289 2008-10 Lynx rufus
# 3 -100.0669 21.50289 2008-12 Lynx rufus
# 4 -100.0669 21.50289 2008-12 Lynx rufus
# 5 -100.0669 21.50289 2008-12 Lynx rufus

The date argument is used to add collection date information, by default this argument is defined as TRUE. While the argument from is still in development and at this moment it has no use.

LR_coords_ndate <- get_species_coords(species = "Lynx rufus", date = FALSE)

head(LR_coords_ndate, n=5)
#        Long      Lat       name
# 1 -100.0494 25.78639 Lynx rufus
# 2 -100.0669 21.50289 Lynx rufus
# 3 -100.0669 21.50289 Lynx rufus
# 4 -100.0669 21.50289 Lynx rufus
# 5 -100.0669 21.50289 Lynx rufus

Downloading the map grid from the SPECIES framework (get_species_grid)

The download of the grid is done with the function get_species_grid, which takes as argument the resolution of the grid, (grid_res). There are 4 possible values for the argument, 8,16,32 and 64.

Mex_grd32 <- get_species_grid(grid_res = 32)

# using ggplot
library(ggplot2)

ggplot(fortify(Mex_grd32), aes(x = long, y = lat, group = id)) +
  geom_polygon() +
  geom_path(color="white") +
  coord_map()

Download model results from the SPECIES platform. (get_species_georel)

The get_species_georel function is used to download the results of the model set in the SPECIES platform. For the moment the function is useful to extract the results of the model for a single species. However, it is possible to use the apply family of functions to extract results from different models (do this operation with care since it can take a lot of time).

# Lynx rufus model with all Mammals
LR_Model <- get_species_georel(target = "Lynx rufus",
                               start_level = "class",
                               value = "Mammalia",
                               validation = FALSE,
                               fossil = FALSE,
                               no_date = TRUE,
                               min_occ = 5,
                               bioclim = FALSE)

head(LR_Model, n = 5)
#    spid                   Specie nij  nj  ni    n Epsilon Score  kingdom
# 1 27318            Canis latrans 106 400 237 9839   31.43  2.68 Animalia
# 2 27360            Taxidea taxus  32  87 237 9839   20.91  3.16 Animalia
# 3 27322 Urocyon cinereoargenteus  85 532 237 9839   20.41  2.04 Animalia
# 4 27635       Lepus californicus  64 382 237 9839   18.29  2.10 Animalia
# 5 27770   Peromyscus maniculatus  99 870 237 9839   17.26  1.65 Animalia
#     phylum    class      order     family
# 1 Craniata Mammalia  Carnivora    Canidae
# 2 Craniata Mammalia  Carnivora Mustelidae
# 3 Craniata Mammalia  Carnivora    Canidae
# 4 Craniata Mammalia Lagomorpha  Leporidae
# 5 Craniata Mammalia   Rodentia Cricetidae

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