In RenaudJau/ChooseRef: Functions for the Durbecq et al. paper (in prep) about ecosystem references

ChooseRef

Functions for the Durbecq et al. paper (in prep) about ecosystem references

How to install the package?

If not yet installed, you should install devtools:

install.packages(devtools)

Load `devtools:

library(devtools) 

Install package ChoosRef:

install_github("RenaudJau/ChooseRef")

And load it:

library(ChooseRef)

How to use the functions?

Here is an example with the dune dataset from vegan package :

library(vegan)
data("dune") #downloading of dune data (cf vegan)
data("dune.env") #downloading of dune.env data (cf vegan)
# keeping only the numeric variables :
dune.env <- data.frame(A1 = dune.env$A1, 
                       Moisture =  as.numeric(as.vector(dune.env$Moisture)),
                       Manure = as.numeric(as.vector(dune.env$Manure)))

# Creating a vector indicating which plots are the potential references and which ones are the restored sites
sites <- factor(c(rep("Rest",5),rep("Ref",15)))
# Creating a vector with the plot names
sites_names <- paste(sites,c(1:5,1:15))
#Poviding names to rows (useful for the outputs)
row.names(dune.env) <- sites_names
row.names(dune) <- sites_names
dune.envRest <- dune.env[sites=="Rest",]
dune.envRef <- dune.env[sites=="Ref",]

So your data.frame should look something like:

• Your restoration sites environmental data:

library(knitr)
data.frame(dune.envRest)

• Your potential references environmental data:

data.frame(dune.envRef)

Calculating reference dissimilarities

Distances <- DissRef3(RELEVES = dune.envRest, REF = dune.envRef, METHOD = "euclidean", DUPLICATES = FALSE)
Distances

Plotting reference dissimilarities

Diss_Ref_Plot(RELEVES = dune.envRest, REF = dune.envRef, DISTANCES = Distances, LINK_NUMBER = "N_REF", N_REF = 3)

RenaudJau/ChooseRef documentation built on April 20, 2020, 10:45 p.m.