humboldt.plot.density: Plot equivalence or background statistic: simulation density...

In jasonleebrown/humboldt: Analysis of Species in Environmental Space

Plot equivalence or background statistic: simulation density curve

Description

Plot equivalence or background statistic: simulation density curve

Usage

humboldt.plot.density(x, type = "D", title = "Background")

Arguments

x	Output from niche equivalence statistic (humboldt.equivalence.stat).
type	Values "D" or "I", which correspond to niche similarity using Schoener's D and Hellinger's I measurements
title	Title of plot

Value

Plots the results from the Background statistic (humboldt.background.stat).

See Also

humboldt.g2e, humboldt.equivalence.stat, humboldt.background.stat, humboldt.niche.similarity, humboldt.plot.niche,humboldt.doitall which use or depend on outputs of this function

Examples

library(humboldt)

##load environmental variables for all sites of the study area 1 (env1). Column names should be x,y,X1,X2,...,Xn)
env1<-read.delim("env1.txt",h=T,sep="\t")

## load environmental variables for all sites of the study area 2 (env2). Column names should be x,y,X1,X2,...,Xn)
env2<-read.delim("env2.txt",h=T,sep="\t") 

## remove NAs and make sure all variables are imported as numbers
env1<-humboldt.scrub.env(env1)
env2<-humboldt.scrub.env(env2)

##load occurrence sites for the species at study area 1 (env1). Column names should be 'sp', 'x','y'
occ.sp1<-na.exclude(read.delim("sp1.txt",h=T,sep="\t"))

##load occurrence sites for the species at study area 2 (env2). Column names should be 'sp', 'x','y'
occ.sp2<-na.exclude(read.delim("sp2.txt",h=T,sep="\t"))

##convert geographic space to espace
zz<-humboldt.g2e(env1=env1, env2=env2, sp1=occ.sp1, sp2=occ.sp2, reduce.env = 2, reductype = "PCA", non.analogous.environments = "NO", env.trim= T, e.var=c(3:21),  col.env = e.var, trim.buffer.sp1 = 200, trim.buffer.sp2 = 200, rarefy.dist = 50, rarefy.units="km", env.reso=0.41666669, kern.smooth = 1, R = 100, run.silent = F)

##perform background statistics 
bg.sp1tosp2<-humboldt.background.stat(g2e=zz, rep = 100, sim.dir = 1, env.reso, kern.smooth = 1, correct.env = F, R = 100, run.silent.bak = F)
bg.sp2tosp1<-humboldt.background.stat(g2e=zz, rep = 100, sim.dir = 2, env.reso, kern.smooth = 1, correct.env = F, R = 100, run.silent.bak = F)

##plot background statistics 
humboldt.plot.density(bg.sp1tosp2,"D","Background 1->2") 
humboldt.plot.density(bg.sp2tosp1,"D","Background 2->1") 

jasonleebrown/humboldt documentation built on Jan. 4, 2024, 7:46 a.m.