humboldt.plot.histrogram: Plot equivalency or background statistics: simulation...

In jasonleebrown/humboldt: Analysis of Species in Environmental Space

Plot equivalency or background statistics: simulation histogram

Description

Plot equivalency or background statistics: simulation histogram

Usage

humboldt.plot.histrogram(x, type = "D", title = "equivalence")

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 output from the equivalence statistic (humboldt.equivalence.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<-na.exclude(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<-na.exclude(read.delim("env2.txt",h=T,sep="\t")) 

##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)

##store espace scores for sp1 and environments 1,2 and both environments combined output from humboldt.g2e
scores.env1<-zz$scores.env1[1:2]
scores.env2<-zz$scores.env2[1:2]
scores.env12<- rbind(zz$scores.env1[1:2],zz$scores.env2[1:2])
scores.sp1<-zz$scores.sp1[1:2]
scores.sp2<-zz$scores.sp2[1:2]

## run create a grid of Environmental Space Function
z1<- humboldt.grid.espace(scores.env12,scores.env1,scores.sp1,kern.smooth=1,R=100)
z2<- humboldt.grid.espace(scores.env12,scores.env2,scores.sp2,kern.smooth=1,R=100)

## run equivalence statistic
a<- humboldt.equivalence.stat(z1,z2,rep=100,kern.smooth=1)

##plot equivalence statistic
humboldt.plot.histrogram(a,"D","Equivalence") 

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