classify.map: Classification of the HSM

In ENiRG: Ecological Niche in R and GRASS

Description

classify.map classifies the Habitat Suitability Map (HSM) using suitability classes.

Usage

classify.map(map, suit.classes, output.name = NULL, load.map = FALSE)

Arguments

map	unclassified suitability map name from GRASS.
suit.classes	object of class boyce, giving the suitability classes.
output.name	string. Name for classified map.
load.map	logical. Whether the map should be uploaded as an object of class raster

Value

Function classify.map allows to classify the HSM according to breaks, which represents limits for intervals in the four suitability classes (unsuitable, marginal, suitable and optimal; Hirzel et al., 2006). Those values can be obtained by using CBI boyce. HSM classified map layer in GRASS can be also uploaded into R by setting load.map to TRUE.

Author(s)

Fernando Canovas [e-mail]

References

Hirzel, A.H., Le Lay, G., Helfer, V., Randin, C., Guisan, A. (2006). Evaluating the ability of the habitat suitability models to predict species presences. Ecological Modelling 199, 142-152.

See Also

enirg, enirg.predict

Examples

## Not run: 
# starting GRASS session
initGRASS("/usr/bin/grass-7.0.0", home=tempdir())
initGRASS("C:/GRASS", home=tempdir())

data(apis.enirg)

# presences table
lina <- apis.enirg$presences

# loading the environmental information in batch
predictor.names <- c("tann", "mxtwm", "mntcm", "rfdm", "rfseas")
predictor.maps <- paste("std_", predictor.names, sep="")
file.names <- paste(system.file(package = "ENiRG"),
                    "/ext/", predictor.names, ".asc", sep="")

import.egvs(file.names, predictor.names)

# standardization
stdz.maps(predictor.names, predictor.maps)

# performing the Ecologigal Niche Factor Analysis (ENFA)
enirg(presences.table = lina, qtegv.maps = predictor.maps,
      species.name = "African", nf = 3, scannf = FALSE,
      method = "normal") -> apis.enfa

enirg.predict(apis.enfa, load.map = TRUE, method = "normal") -> apis.hsm

data(cbi.results)

classify.map(map = "African_predicted_hsm",
             suit.classes = cbi.results,
             output.name = "African_hsm_class") -> apis.hsm.class

## End(Not run)

ENiRG documentation built on May 1, 2019, 9:15 p.m.