minosse.poly: The species geographic range polygon

In francesco-carotenuto/PaleoMacroEco: Methods and Tools for Deep-Time Macroecology with Fossil Data

Description

This function turns MInOSSE geographic range raster map into a spatial polygon with the related surface area.

Usage

minosse.poly(minosse_res, th_num=3)

Arguments

minosse_res	the output of minosse.target function or the minosse_res element list in the minosse function output.
th_num	Numeric. The Regression Kriging prediction map binarization threshold value index as reported in the optimal.thresholds function in the PresenceAbsence package. Default 3 = MaxSens+Spec, maximizes (sensitivity+specificity)/2.

Value

the target species geographic range as a SpatialPolygonsDataFrame object.

Author(s)

Francesco Carotenuto, [e-mail]

Examples

  
  library(raster)
  data(lgm)
  raster(system.file("exdata/prediction_ground.gri", package="DeepTime"))->prediction_ground

  minosse_dat<-minosse.data(obj=lgm,species_name="Mammuthus_primigenius",
  domain="land",coc.by="locality",min.occs=3,abiotic.covs=NULL,
  combine.covs=FALSE,reduce_covs_by="pca",covs_th=0.95,c.size="mean",
  bkg.predictors="presence",min.bkg=100,sampling.by.distance=TRUE,
  crop.by.mcp=FALSE,prediction.ground=prediction_ground,projection="laea",
  lon_0=85,lat_0=45,n.clusters="automatic",seed=625)

  minosse_res<-minosse.target(resp=minosse_dat[[1]],predictors=minosse_dat[[2]],
  bkg="presence", min.bkg = 100,n.sims=10,sampling.by.distance=TRUE,n.folds=1,
  n.sims.clusters="automatic",seed=625)

  minosse.poly(minosse_res)
  

francesco-carotenuto/PaleoMacroEco documentation built on Dec. 23, 2019, 6:36 p.m.