mafragh {ade4}R Documentation

Phyto-Ecological Survey

Description

This data set gives environmental and spatial informations about species and sites.

Usage

data(mafragh)

Format

mafragh is a list of 6 components.

xy
are the coordinates of 97 sites.
flo
is a data frame with 97 sites and 56 species.
espnames
is a vector of the names of species.
neig
is the neighbourhood graph of the 97 sites (an object of class 'neig').
mil
is a data frame with 97 sites and 11 environmental variables.
partition
is a factor classifying the 97 sites in 5 classes.
area
is a data frame of class area

Source

Belair, G.d. and Bencheikh-Lehocine, M. (1987) Composition et déterminisme de la végétation d'une plaine côtière marécageuse : La Mafragh (Annaba, Algérie). Bulletin d'Ecologie, 18, 393–407.

References

See a data description at http://pbil.univ-lyon1.fr/R/pps/pps053.pdf (in French).

Examples

data(mafragh)
par(mfrow = c(3,2))
s.label(mafragh$xy, inc = FALSE, neig = mafragh$neig, 
    sub = "Samples & Neighbourhood graph")
coa1 <- dudi.coa(mafragh$flo, scan = FALSE)
s.value(mafragh$xy, coa1$li[,1], sub = "Axis 1 - COA")
pca1 <- dudi.pca(mafragh$xy, scan = FALSE)
s.value(mafragh$xy, pca1$li[,1], sub = "Axis 1 - PCA")
s.class(pca1$li, mafragh$partition, sub = "Plane 1-2 - PCA")
s.class(coa1$li, mafragh$partition, sub = "Plane 1-2 - COA")
s.chull(mafragh$xy, mafragh$partition, optchull = 1)
par(mfrow=c(1,1))

## Not run: 
link1 <- area2link(mafragh$area)
neig1 <- neig(mat01 = 1*(link1>0))
nb1 <- neig2nb(neig1)
par(mfrow = c(2,1))
area.plot(mafragh$area,center = mafragh$xy,clab=0.75)
area.plot(mafragh$area,center = mafragh$xy,graph=neig1)
if (require(maptools, quiet = TRUE) & require(spdep, quiet = TRUE)) {
    lw1 <- apply(link1,1,function(x) x[x>0])
    listw1 <- nb2listw(nb1,lw1)
    coa1 <- dudi.coa(mafragh$flo, scan = FALSE, nf = 4)
    ms1 <- multispati(coa1, listw1, scan = FALSE, nfp = 2, nfn = 0)
    summary(ms1)
    par(mfrow = c(2,2))
    barplot(coa1$eig)
    barplot(ms1$eig)
    s.corcircle(ms1$as)
    plot(coa1$li[,1], ms1$li[,1])
}
par(mfrow = c(1,1))

## End(Not run)

Worked out examples


> library(ade4)
> ### Name: mafragh
> ### Title: Phyto-Ecological Survey
> ### Aliases: mafragh
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(mafragh)
> par(mfrow = c(3,2))
> s.label(mafragh$xy, inc = FALSE, neig = mafragh$neig, 
+     sub = "Samples & Neighbourhood graph")
> coa1 <- dudi.coa(mafragh$flo, scan = FALSE)
> s.value(mafragh$xy, coa1$li[,1], sub = "Axis 1 - COA")
> pca1 <- dudi.pca(mafragh$xy, scan = FALSE)
> s.value(mafragh$xy, pca1$li[,1], sub = "Axis 1 - PCA")
> s.class(pca1$li, mafragh$partition, sub = "Plane 1-2 - PCA")
> s.class(coa1$li, mafragh$partition, sub = "Plane 1-2 - COA")
> s.chull(mafragh$xy, mafragh$partition, optchull = 1)
> par(mfrow=c(1,1))
> 
> link1 <- area2link(mafragh$area)
> neig1 <- neig(mat01 = 1*(link1>0))
> nb1 <- neig2nb(neig1)
> par(mfrow = c(2,1))
> area.plot(mafragh$area,center = mafragh$xy,clab=0.75)
> area.plot(mafragh$area,center = mafragh$xy,graph=neig1)
> if (require(maptools, quiet = TRUE) & require(spdep, quiet = TRUE)) {
+     lw1 <- apply(link1,1,function(x) x[x>0])
+     listw1 <- nb2listw(nb1,lw1)
+     coa1 <- dudi.coa(mafragh$flo, scan = FALSE, nf = 4)
+     ms1 <- multispati(coa1, listw1, scan = FALSE, nfp = 2, nfn = 0)
+     summary(ms1)
+     par(mfrow = c(2,2))
+     barplot(coa1$eig)
+     barplot(ms1$eig)
+     s.corcircle(ms1$as)
+     plot(coa1$li[,1], ms1$li[,1])
+ }
deldir 0.0-12 

     Please note: The process for determining duplicated points
     has changed from that used in version 0.0-9 (and previously).


Multivariate Spatial Analysis
Call: multispati(dudi = coa1, listw = listw1, scannf = FALSE, nfposi = 2, 
    nfnega = 0)

Scores from the initial duality diagramm:
          var       cum     ratio     moran
RS1 0.8691476 0.8691476 0.1043473 0.7493283
RS2 0.6491089 1.5182565 0.1822775 0.5236761
RS3 0.5975380 2.1157944 0.2540161 0.2857733
RS4 0.4627802 2.5785747 0.3095762 0.3234089

Multispati eigenvalues decomposition:
          eig       var     moran
CS1 0.7063862 0.8354536 0.8455122
CS2 0.3973350 0.5928146 0.6702518
> par(mfrow = c(1,1))
> 
> 
> 
> 

[Package ade4 Index]