minosse.plot: A function to plot the MInOSSE results

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

Description

This function provides two maps: one with a species occurrence probability and another with the binarized geographic range

Usage

minosse.plot(minosse_res,th_num=3,pcex=1.5,cont_pol=NULL,title=NULL)

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.
pcex	Numeric. The graphic parameter indicating the size of points showing target species fossil localities. Default 1.5.
cont_pol	The spatial polygon object showing the land or sea contour on the maps. Default NULL.
title	The title on the top of the plot. If NULL, then the name of the species is used. Default NULL

Details

When running this function for the first time in your workspece it is necessary to firstly load ggplo2.

Value

A plot showing the occurrence probability (on the left) and the threshold-based gepgraphic range (on the right) maps of target species along with its fossil localities.

Author(s)

Francesco Carotenuto, [e-mail]

Examples

  

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

  mam<-minosse(dat=lgm,species.name="Mammuthus_primigenius",domain="land",
  prediction.ground=prediction_ground,crop.by.mcp=FALSE,th_num=3,
  coc_by="locality",n.sims=10,projection="laea",lon_0 = 85,
  lat_0 = 45,seed=625)

  library(ggplot2)
  minosse.plot(mam)

  

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