niche: Method to Analyse a pair of tables : Environmental and...

nicheR Documentation

Method to Analyse a pair of tables : Environmental and Faunistic Data

Description

performs a special multivariate analysis for ecological data.

Usage

niche(dudiX, Y, scannf = TRUE, nf = 2)
## S3 method for class 'niche'
print(x, ...) 
## S3 method for class 'niche'
plot(x, xax = 1, yax = 2, ...)
niche.param(x)
## S3 method for class 'niche'
rtest(xtest,nrepet=99, ...)

Arguments

dudiX

a duality diagram providing from a function dudi.coa, dudi.pca, ... using an array sites-variables

Y

a data frame sites-species according to dudiX$tab with no columns of zero

scannf

a logical value indicating whether the eigenvalues bar plot should be displayed

nf

if scannf FALSE, an integer indicating the number of kept axes

x

an object of class niche

...

further arguments passed to or from other methods

xax, yax

the numbers of the x-axis and the y-axis

xtest

an object of class niche

nrepet

the number of permutations for the testing procedure

Value

Returns a list of the class niche (sub-class of dudi) containing :

rank

an integer indicating the rank of the studied matrix

nf

an integer indicating the number of kept axes

RV

a numeric value indicating the RV coefficient

eig

a numeric vector with the all eigenvalues

lw

a data frame with the row weigths (crossed array)

tab

a data frame with the crossed array (averaging species/sites)

li

a data frame with the species coordinates

l1

a data frame with the species normed scores

co

a data frame with the variable coordinates

c1

a data frame with the variable normed scores

ls

a data frame with the site coordinates

as

a data frame with the axis upon niche axis

Author(s)

Daniel Chessel
Anne-Béatrice Dufour anne-beatrice.dufour@univ-lyon1.fr
Stéphane Dray stephane.dray@univ-lyon1.fr

References

Dolédec, S., Chessel, D. and Gimaret, C. (2000) Niche separation in community analysis: a new method. Ecology, 81, 2914–1927.

Examples

data(doubs)
dudi1 <- dudi.pca(doubs$env, scale = TRUE, scan = FALSE, nf = 3)
nic1 <- niche(dudi1, doubs$fish, scann = FALSE)

if(adegraphicsLoaded()) {
  g1 <- s.traject(dudi1$li, plab.cex = 0, plot = FALSE)
  g2 <- s.traject(nic1$ls, plab.cex = 0, plot = FALSE)
  g3 <- s.corcircle(nic1$as, plot = FALSE)
  g4 <- s.arrow(nic1$c1, plot = FALSE)
  G1 <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2))
  
  glist <- list()
  for(i in 1:ncol(doubs$fish))
    glist[[i]] <- s.distri(nic1$ls, dfdistri = doubs$fish[, i], psub.text = names(doubs$fish)[i], 
      plot = FALSE, storeData = TRUE)
  G2 <- ADEgS(glist, layout = c(5, 6))
  
  G3 <- s.arrow(nic1$li, plab.cex = 0.7)  
    
} else {
  par(mfrow = c(2, 2))
  s.traject(dudi1$li, clab = 0)
  s.traject(nic1$ls, clab = 0)
  s.corcircle(nic1$as)
  s.arrow(nic1$c1)

  par(mfrow = c(5, 6))
  for (i in 1:27) s.distri(nic1$ls, as.data.frame(doubs$fish[,i]),
    csub = 2, sub = names(doubs$fish)[i])
    
  par(mfrow = c(1, 1))
  s.arrow(nic1$li, clab = 0.7)

}

data(trichometeo)
pca1 <- dudi.pca(trichometeo$meteo, scan = FALSE)
nic1 <- niche(pca1, log(trichometeo$fau + 1), scan = FALSE)
plot(nic1)
niche.param(nic1)
rtest(nic1,19)

data(rpjdl)
plot(niche(dudi.pca(rpjdl$mil, scan = FALSE), rpjdl$fau, scan = FALSE))

ade4 documentation built on Nov. 2, 2022, 1:07 a.m.

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