enirg.plot: Ordination plot of 'enirg' results
In ENiRG: Ecological Niche in R and GRASS

Description Usage Arguments Details Author(s) References See Also Examples

Performs an ordination diagram for objects of class enirg.

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enirg.plot(enirg.results, mar.col = "grey", spe.col = "black",
           method = "extended", plot.egvs = TRUE, asp = FALSE,
           title = NULL)

`enirg.results`	an object of class `enirg`
`mar.col`	color for filling available space (habitat)
`spe.col`	color for filling used space (presences data)
`method`	a string character. "extended" represents available space by using the convex hull, "simplified" represents available space by a polygon, representing the range.
`plot.egvs`	logical. If TRUE, ecogeographical variables will be also plotted in the ordination diagram.
`asp`	logical. If TRUE, marginality and specialization axes will be scaled.
`title`	string. A title for plot.

enirg.plot displays the factorial map of pixels, by projection of the row coordinates of ENFA analysis. Available and used habitat are displayed as polygon area and clouds of points, respectively. Marginality axis is the X-axis and specialization is the Y-axis. Quantitative environmental predictors used for the analysis are represented using blue arrows and qualitative ones are represented by text labels. White dot shows the centroid of the used habitat.

Fernando Canovas fcgarcia@ualg.pt, Chiara Magliozzi chiara.magliozzi@libero.it

Basille, M., Calenge, C., Marboutin, E., Andersen, R. and Gaillard, J.M. (2008) Assessing habitat selection using multivariate statistics: Some refinements of the ecological-niche factor analysis. Ecological Modelling, 211, 233–240.

enirg, import.egvs, enfa, scatter.enfa, initGRASS

## 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.plot(apis.enfa)


## End(Not run)