suprow: Projections of Supplementary Rows

In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

Description

performs projections of supplementary rows.

Usage

 
## S3 method for class 'coa'
suprow(x, Xsup, ...) 
## S3 method for class 'dudi'
suprow(x, Xsup, ...) 
## S3 method for class 'pca'
suprow(x, Xsup, ...) 

Arguments

x	an object of class dudi
Xsup	an array with the supplementary rows (Xsup and x$tab have the same column number)
...	further arguments passed to or from other methods

Details

If suprow.dudi is used, the column vectors of Xsup are projected without prior modifications onto the principal components of dudi with the scalar product associated to the row weightings of dudi.

Value

returns a data frame containing the coordinates of the supplementary projections

Author(s)

Daniel Chessel
Anne B Dufour [e-mail]

References

Gower, J. C. (1967) Multivariate analysis and multivariate geometry. The statistician, 17, 13–28.

Examples

data(euro123)
par(mfrow = c(2, 2))
w <- euro123[[2]]
dudi1 <- dudi.pca(w, scal = FALSE, scan = FALSE)

if(adegraphicsLoaded()) {
  g11 <- s.arrow(dudi1$c1, psub.text = "Classical", psub.posi = "bottomright", plot = FALSE)
  g12 <- s.label(suprow(dudi1, w)$tabsup, plab.cex = 0.75, plot = FALSE)
  g1 <- superpose(g11, g12)
  
  g21 <- s.arrow(dudi1$c1, psub.text = "Without centring", psub.posi = "bottomright", plot = FALSE)
  g22 <- s.label(suprow(dudi1, w)$tabsup, plab.cex = 0.75, plot = FALSE)
  g2 <- superpose(g21, g22) 
  
  g3 <- triangle.label(w, plab.cex = 0.75, label = row.names(w), adjust = FALSE, plot = FALSE)
  g4 <- triangle.label(w, plab.cex = 0.75, label = row.names(w), adjust = TRUE, plot = FALSE)
  
  G <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2))
  
} else {
  s.arrow(dudi1$c1, sub = "Classical", possub = "bottomright", csub = 2.5)
  s.label(suprow(dudi1, w), add.plot = TRUE, clab = 0.75)
  
  s.arrow(dudi1$c1, sub = "Without centring", possub = "bottomright", csub = 2.5)
  s.label(suprow(dudi1, w), clab = 0.75, add.plot = TRUE)
  
  triangle.plot(w, clab = 0.75, label = row.names(w), scal = FALSE)
  triangle.plot(w, clab = 0.75, label = row.names(w), scal = TRUE)
}

data(rpjdl)
rpjdl.coa <- dudi.coa(rpjdl$fau, scann = FALSE, nf = 4)
rpjdl.coa$li[1:3, ]
suprow(rpjdl.coa,rpjdl$fau[1:3, ])$lisup  #the same

data(deug)
deug.dudi <- dudi.pca(df = deug$tab, center = deug$cent, scale = FALSE, scannf = FALSE)
suprow(deug.dudi, deug$tab[1:3, ])$lisup  #the supplementary individuals are centered
deug.dudi$li[1:3, ]  # the same

Example output

     Axis1       Axis2      Axis3      Axis4
1 1.449656 -1.59644004 -1.2912481 -2.0346309
2 1.308057 -1.56619615 -1.2428411 -1.6905682
3 1.042200  0.00201931 -0.2788701 -0.1574388
     Axis1       Axis2      Axis3      Axis4
1 1.449656 -1.59644004 -1.2912481 -2.0346309
2 1.308057 -1.56619615 -1.2428411 -1.6905682
3 1.042200  0.00201931 -0.2788701 -0.1574388
     Axis1      Axis2
1 14.86352 -12.399345
2 16.49579   8.738351
3 21.97732   9.038219
     Axis1      Axis2
1 14.86352 -12.399345
2 16.49579   8.738351
3 21.97732   9.038219

ade4 documentation built on May 2, 2019, 5:50 p.m.