humboldt.occ.rarefy: Rarefy occurrence points

In jasonleebrown/humboldt: Analysis of Species in Environmental Space

Rarefy occurrence points

Description

Rarefy occurrence points

Usage

humboldt.occ.rarefy(
  in.pts,
  colxy = 2:3,
  rarefy.dist = 0,
  rarefy.units = "km",
  run.silent.rar = F
)

Arguments

in.pts	input data frame
colxy	columns corresponding to longitude and latitude
rarefy.dist	distance to rarefy points (values need to be in km[recommended] or decimal degrees). See associated parameter rarefy.units.
rarefy.units	the units of rarefy.dist parameter, either "km" for kilometers or "dd" for decimal degrees
run.silent.rar	if run.silent=T, texts boxes displaying progress will not be displayed

Value

A script to systematically select localities within a specified area at specified spatial resolution. The outcome is always the same and is not random. This reduces sampling biases in downstream analyses- you should do it! Output is a reduced dataset with less spatial autocorrelation.

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"))

##remove occurrences closer than a minimum distance to each other (remove aggregation). Setting min.dist=0 will remove no occurrence.
occ.sp1<-humboldt.occ.rarefy(in.pts=occ.sp1,colxy=2:3, rarefy.dist = 50, rarefy.units = "km")
occ.sp2<-humboldt.occ.rarefy(in.pts=occ.sp2,colxy=2:3, rarefy.dist = 50, rarefy.units = "km")

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