README.md

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:

##         A1 Moisture Manure
## Rest 1 2.8        1      4
## Rest 2 3.5        1      2
## Rest 3 4.3        2      4
## Rest 4 4.2        2      4
## Rest 5 6.3        1      2

• Your potential references environmental data:

##          A1 Moisture Manure
## Ref 1   4.3        1      2
## Ref 2   2.8        1      3
## Ref 3   4.2        5      3
## Ref 4   3.7        4      1
## Ref 5   3.3        2      1
## Ref 6   3.5        1      1
## Ref 7   5.8        4      2
## Ref 8   6.0        5      3
## Ref 9   9.3        5      0
## Ref 10 11.5        5      0
## Ref 11  5.7        5      3
## Ref 12  4.0        2      0
## Ref 13  4.6        1      0
## Ref 14  3.7        5      0
## Ref 15  3.5        5      0

Calculating reference dissimilarities

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

## $Diss_Mean
## [1] 4.835113 3.672444 4.124837 4.133419 4.034573
## 
## $Diss_Min
## [1] 1.000000 0.800000 2.061553 1.989975 2.000000
## 
## $RelRef_order
##           X1     X2    X3    X4     X5     X6     X7     X8    X9    X10    X11
## Rest 1 Ref 2  Ref 1 Ref 6 Ref 5 Ref 12  Ref 4  Ref 3 Ref 13 Ref 7 Ref 11  Ref 8
## Rest 2 Ref 1  Ref 6 Ref 2 Ref 5 Ref 13 Ref 12  Ref 4  Ref 7 Ref 3 Ref 15 Ref 14
## Rest 3 Ref 2  Ref 1 Ref 5 Ref 3  Ref 7  Ref 6 Ref 11  Ref 8 Ref 4 Ref 12 Ref 13
## Rest 4 Ref 2  Ref 1 Ref 5 Ref 3  Ref 6  Ref 7 Ref 11  Ref 8 Ref 4 Ref 12 Ref 13
## Rest 5 Ref 1 Ref 13 Ref 6 Ref 7 Ref 12  Ref 5  Ref 2  Ref 4 Ref 8 Ref 11  Ref 3
##           X12    X13   X14    X15
## Rest 1 Ref 15 Ref 14 Ref 9 Ref 10
## Rest 2 Ref 11  Ref 8 Ref 9 Ref 10
## Rest 3 Ref 14 Ref 15 Ref 9 Ref 10
## Rest 4 Ref 14 Ref 15 Ref 9 Ref 10
## Rest 5 Ref 14 Ref 15 Ref 9 Ref 10
## 
## $DistRef_order
##              X1       X2       X3       X4       X5       X6       X7       X8
## Rest 1 1.000000 2.500000 3.080584 3.201562 4.294182 4.337050 4.354308 4.386342
## Rest 2 0.800000 1.000000 1.220656 1.428286 2.282542 2.291288 3.168596 3.780212
## Rest 3 2.061553 2.236068 3.162278 3.163858 3.201562 3.261901 3.458323 3.590265
## Rest 4 1.989975 2.238303 3.132092 3.162278 3.238827 3.249615 3.500000 3.638681
## Rest 5 2.000000 2.624881 2.973214 3.041381 3.207803 3.316625 3.640055 4.093898
##              X9      X10      X11      X12      X13      X14       X15
## Rest 1 4.690416 5.040833 5.219195 5.700000 5.728001 8.616844 10.377379
## Rest 2 4.182105 4.472136 4.476606 4.673329 4.821825 7.323933  9.165151
## Rest 3 3.655133 4.011234 4.134005 5.035871 5.063596 7.071068  8.765843
## Rest 4 3.640055 4.004997 4.142463 5.024938 5.048762 7.142129  8.848164
## Rest 5 4.134005 4.166533 4.627094 5.173007 5.276362 5.385165  6.858571

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.