DissRef3: Similarities between references and restoration

In RenaudJau/Renaudpack2: Un fourre tout de mes fonctions...

Description

Calculate similarity between plots and a group of reference plot

Usage

DissRef3(RELEVES, REF, METHOD = "bray", BINARY = FALSE, DUPLICATES = TRUE)

Arguments

RELEVES	Variables of the restoration sites data matrix
REF	Variables surveys of reference sites data matrix
METHOD	Dissimilarity index, partial match to "manhattan", "euclidean", "canberra", "clark", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup", "binomial", "chao", "cao" or "mahalanobis". Cf vegan::vegdist function
BINARY	(FALSE by default) If TRUE, data is converted to binary data
DUPLICATES	(TRUE by default) Are REF plots also included in RELEVES data?

Value

Diss_Mean	average dissimilarity by RELEVES
Diss_Min	minimal dissimilarity by RELEVES
RelRef_order	list of REF names in ascending order of dissimilarity for each RELEVES
DistRef_order	list of REF distance values in ascending order of dissimilarity for each RELEVES

Examples

# ------------  Creating the data needed for the example --------------------
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",]

# --------------  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/Renaudpack2 documentation built on Dec. 12, 2020, 5:14 a.m.