map.easy: Species distributions made easy (multiple species).

Description Usage Arguments Value References

View source: R/red.R

Description

Single step for prediction of multiple species distributions. Output of maps (in pdf format), klms (for Google Earth) and relevant data (in csv format).

Usage

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map.easy(longlat, layers = NULL, habitat = NULL, zone = NULL,
  error = NULL, move = TRUE, dem = NULL, pca = 0, filename = NULL,
  mapoption = NULL, testpercentage = 0, mintest = 20, runs = 0,
  subset = 0)

Arguments

longlat

data.frame of taxon names, longitude and latitude or eastness and northness (three columns in this order) of each occurrence record.

layers

If NULL analyses are done with environmental layers read from data files of red.setup(). If a Raster* object as defined by package raster, analyses use these.

habitat

Raster* object as defined by package raster. Habitat extent layer (0/1) used instead of layers if any species is an habitat specialist.

zone

UTM zone if data is in metric units. Used only for correct placement of kmls and countries.

error

Vector of spatial error in longlat (one element per row of longlat) in the same unit as longlat. Used to move any point randomly within the error radius.

move

If TRUE, identifies and moves presence records to closest cells with environmental data. Use when spatial error might put records outside such data.

dem

RasterLayer object. It should be a digital elevation model for calculation of elevation limits of the species. If NULL, dem from red.setup() is used if possible, otherwise it will be 0.

pca

Number of pca axes for environmental data reduction. If 0 (default) no pca is made.

filename

Name of output csv file with all results. If NULL it is named "Results_All.csv".

mapoption

Vector of values within options: points, habitat and sdm; each value corresponding to the function to be used for each species (map.points, map.habitat, map.sdm). If a single value, all species will be modelled according to it. If NULL, the function will perform analyses using map.points. Species values must be in same order as latlong.

testpercentage

Percentage of records used for testing only. If 0 all records will be used for both training and testing.

mintest

Minimim number of total occurrence records of any species to set aside a test set. Only used if testpercentage > 0.

runs

If <= 0 no ensemble modelling is performed. If > 0, ensemble modelling with n runs is made. For each run, a new random sample of occurrence records (if testpercentage > 0), background points and predictive variables (if subset > 0) are chosen. In the ensemble model, each run is weighted as max(0, (runAUC - 0.5)) ^ 2.

subset

Number of predictive variables to be randomly selected from layers for each run if runs > 0. If <= 0 all layers are used on all runs. Using a small number of layers is usually better than using many variables for rare species, with few occurrence records (Lomba et al. 2010, Breiner et al. 2015).

Value

Outputs maps in asc, pdf and kml format, plus a file with EOO, AOO and a list of countries where the species is predicted to be present if possible to extract.

References

Breiner, F.T., Guisan, A., Bergamini, A., Nobis, M.P. (2015) Overcoming limitations of modelling rare species by using ensembles of small models. Methods in Ecology and Evolution, 6: 1210-1218.

Lomba, A., Pellissier, L., Randin, C.F., Vicente, J., Moreira, F., Honrado, J., Guisan, A. (2010) Overcoming the rare species modelling paradox: a novel hierarchical framework applied to an Iberian endemic plant. Biological Conservation, 143: 2647-2657.


red documentation built on July 28, 2017, 5:02 p.m.

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