Vignette Data Prepare

In bossMaps: Convert Binary Species Range Maps into Continuous Surfaces Based on Distance to Range Edge

knitr::opts_chunk$set(cache=T,fig.width=5,fig.height=5,dpi=125)

Packages

# packages used for the data generation
library(raster)
library(rasterVis)
library(tidyr)
library(dplyr)
library(geosphere)
library(maptools)
library(mapdata)
library(bossMaps)
library(rMOL)

Install rMOL and bossMaps packages

#devtools::install_github("MapofLife/rMOL")#, ref="7622634")
#devtools::install_github("adammwilson/bossMaps",)
#devtools::install_local("~/repos/bossMaps_0.1.tgz")

Download Worldclim bioclim variables

env=getData('worldclim', var='bio', res=10)
env=env[[c(1,12)]]

Define modelling domain as the worldclim grid

domain=raster(env,layer=0)

Download Species data

species=c("Tinamus_solitarius")

dsp=MOLget(species,type=c("points","range"))
plot(env[[1]]);plot(dsp$points,add=T);plot(dsp$range,add=T,border="red")

crude cleaning of species data (within 1000km of expert range)

dsp=MOLclean(dsp,dropdist=1000,drop=T)
plot(env[[1]]);plot(dsp$points,add=T);plot(dsp$range,add=T,border="red")

Extract range and points

points=dsp$points
range=dsp$range

Calculate range distances

fdist=paste0(species,"_rangeDist.tif")
  if(!file.exists(fdist)) {
    ## calculate distance-to-range: this is slow but only has to be done once per species.
    ## Can speed it up by increasing fact (at the expense of lower accuracy).
    rdist=rangeDist(range,points,domain,domainkm=3000,mask=F,fact=2)    
    ## Mask out undesired areas (ocean, etc.)
    ## Typically you would do this using your environmental data,
    ## but here we'll just use a coastline polygon from the maps package
  land=map(interior=F,fill=T,xlim=bbox(rdist)[1,],ylim=bbox(rdist)[2,],plot=F)
  land=map2SpatialPolygons(land,IDs=land$names)

  rdist=mask(rdist,land)
  rdist=trim(rdist,padding=10,file=fdist,overwrite=T)
  }

rdist=raster(fdist)
names(rdist)="rangeDist"



plot(rdist);plot(range,add=T);plot(points,add=T)

Process environmental data

  fo=paste0(species,"_env.grd")
  if(!file.exists(fo)){
  land=map(interior=F,fill=T,xlim=bbox(rdist)[1,],ylim=bbox(rdist)[2,],plot=F)
  land=map2SpatialPolygons(land,IDs=land$names)
    td=crop(env,rdist)
      mask(td,land,file=fo,overwrite=T)
      senv=writeRaster(td,file=sub("env","senv",fo),overwrite=T)
}
senv=stack(sub("env","senv",fo))
plot(senv)

Save the data to the package

Tinamus_solitarius_env=readAll(senv)
devtools::use_data(Tinamus_solitarius_env)

Tinamus_solitarius_points=points
Tinamus_solitarius_range=range

#save it
devtools::use_data(Tinamus_solitarius_points,overwrite=T)
devtools::use_data(Tinamus_solitarius_range,overwrite=T)

bossMaps documentation built on May 2, 2019, 3:57 p.m.