# niche: Method to Analyse a pair of tables : Environmental and... In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

 niche R 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)

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 Feb. 16, 2023, 7:58 p.m.