humboldt.sample.spp: Sample environment to occurrence points

In jasonleebrown/humboldt: Analysis of Species in Environmental Space

Sample environment to occurrence points

Description

Sample environment to occurrence points

Usage

humboldt.sample.spp(
  dfsp,
  colspxy = 2:3,
  colspkept = "xy",
  dfvar,
  colvarxy = 1:2,
  colvar = "all",
  resolution,
  run.silent.sam = F
)

Arguments

dfsp	Data frame of species with x, y and optional other variables
colspxy	The range of columns corresponding to longitude and latitude
colspkept	Columns to include in output from species dataset (default="xy")
dfvar	Environmental data frame with x, y and environmental variables
colvarxy	The range of columns for x and y in dfvar
colvar	The range of environmental variables columns in dfvar (excluding "xy", NULL=all)
resolution	of environmental data (typically in decimal degrees)
run.silent.sam=F	If run.silent.sam=T, texts boxes displaying progress will not be displayed. Default value is FASLE.

Value

A simple function to sample input environmental data corresponding sites of input occurrence points. Output is a table with environmental variables for each input locality (minus sites with no or missing environmental data).

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=40, rarefy.units="km")
occ.sp2<-humboldt.occ.rarefy(in.pts=occ.sp2,colxy=2:3, rarefy.dist=40, rarefy.units="km")

##sample environment using humboldt.sample.sp() function
## env.reso should be the resolution of the environmental data grid
env.reso=0.41666669 
occ.sp1<-na.exclude(humboldt.sample.spp(dfsp=occ.sp1,colspxy=2:3,colspkept=NULL,dfvar=env1,colvarxy=1:2,colvar="all",resolution=env.reso))
occ.sp2<-na.exclude(humboldt.sample.spp(dfsp=occ.sp2,colspxy=2:3,colspkept=NULL,dfvar=env2,colvarxy=1:2,colvar="all",resolution=env.reso))

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