twoHmax {adiv}R Documentation

Maximization of the Diversity Index TwoH

Description

The R function twoHmax maximizes function 2H (Pavoine and Izsak 2014) for a given matrix C of (functional or phylogenetic) similarities between species. It is based on function divcmax of the ade4 package in R. As function divcmax of package ade4, function twoHmax uses an optimization technique based on Rosen's projection gradient algorithm and is verified using the Kuhn-Tucker conditions.

Usage

twoHmax(C, epsilon = 1e-08, smooth = TRUE, comment = FALSE)

Arguments

C

a matrix that contains measures of the chosen intraspecific components (see functions CFprop, multiCFprop, CFbinary, multiCFbinary) on the diagonal and measures of interspecific components off diagonal. These interspecific components reflect functional or phylogenetic similarities among species.

epsilon

a numeric tolerance threshold: a frequency is non null if it is higher than epsilon.

smooth

a logical value: if TRUE, the estimated positive proportions are checked and re-estimated with exact matrix products.

comment

a logical value indicating whether or not comments on the optimization technique should be printed.

Value

A list of two objects:

value

the maximum value of index 2H (see function qHdiv);

vector

a data frame with the vector pmax that maximizes index 2H (see function qHdiv).

Author(s)

Sandrine Pavoine sandrine.pavoine@mnhn.fr

The code is a modification of function divcmax of package ade4 written by Stephane Champely.

References

Pavoine, S. and Izsak, J. (2014) New biodiversity measure that includes consistent interspecific and intraspecific components. Methods in Ecology and Evolution, 5, 165–172.

See Also

qHdiv, CFprop, CFbinary

Examples

## Not run: 
if(require(ape)){

tre <-"((((((sA:4,sB:1):1,sC:3):2,((sD:2,sE:1):1,sF:1):2):1,sG:7):1,sH:1):3,(sI:2,sJ:1):2):0;"
#The number of tips is kept in parameter n:
n<-10
# Next we need to obtain matrix CP. 
phyape <- read.tree(text = tre)
plot(phyape)
CP <- vcv(phyape)
WP <- diag(diag(CP))
# With this particular illustration, a maximizing vector, 
# for 2H used with CP, that does not contain any zero can be found. 
# This maximizing vector can thus be obtained directly, 
# instead of being estimated. Two equivalent equations 
# have been given to obtain the maximizing vector in 
# Appendix S1 of Pavoine and Izsak (2014). 
# We use the first one below
Pmax<-(solve(CP^2)%*%diag(CP))/sum(solve(CP^2)%*%diag(CP))
Pmax

# The second equation equivalently provides
Z <- ((diag(1/sqrt(diag(CP))))%*%CP%*%(diag(1/sqrt(diag(CP)))))^2
Pmax<-(solve(WP)%*%solve(Z)%*%rep(1,n))/sum(solve(WP)%*%solve(Z))
Pmax

# Applied to our case study, the function twoHmax provides good approximations
twoHmax(CP)

# Redundancy among variables:
data(rhone, package="ade4")
V <- rhone$tab
# First consider the covariances among the variables:
C <- cov(V)
# A vector that maximizes 2H applied to C is estimated as follows:
pmax_covariances <- twoHmax(C)$vector
dotchart(as.matrix(pmax_covariances))

# If we apply 2H only to the diagonal matrix with the variances 
# of the variables, the vector that maximizes 2H is:
W <- diag(diag(C))
rownames(W)<-colnames(W)<-rownames(C)
pmax_variances <- twoHmax(W)$vector
dotchart(as.matrix(pmax_variances))

# If C contains the correlations among variables, 
# a vector that maximizes 2H applied to C is estimated as follows:
C <- cor(V)
pmax_correlations <- twoHmax(C)$vector
dotchart(as.matrix(pmax_correlations))


# By attributing equal weights to the variables, 
# 2H applied to the correlation matrix measures 
# the number of effective variables:
# from 0 if all variables are completely correlated 
# with each other to n if they are not correlated. 
# Similarly, by attributing equal weights to the variables, 
# 2H applied to the covariance matrix measures
# the effective amount of variation:
# from 0 if all variables are completely correlated 
# with each other to n if they are not correlated 
# and have similar variances.

#Even if the data set contains 15 variables, 
# the effective number of variables is lower.
C <- cor(V)
equalproportions <- cbind.data.frame(rep(1/ncol(C), ncol(C)))
names(equalproportions) <- "equalprop"
equalproportions <- t(equalproportions)
qHdiv(equalproportions, C)

# When considering the covariances among species, 
# instead of the correlations, the effective number 
# of variables is even lower, indicating also an imbalance 
# in the variances of the variables.
C <- cov(V)
qHdiv(equalproportions, C)

}

## End(Not run)

[Package adiv version 2.1.1 Index]