ade4 (version 1.7-22)

baran95: African Estuary Fishes

Description

This data set is a list containing relations between sites and fish species linked to dates.

Usage

data(baran95)

Format

This list contains the following objects:

fau

is a data frame 95 seinings and 33 fish species.

plan

is a data frame 2 factors : date and site. The date has 6 levels (april 1993, june 1993, august 1993, october 1993, december 1993 and february 1994) and the sites are defined by 4 distances to the Atlantic Ocean (km03, km17, km33 and km46).

species.names

is a vector of species latin names.

References

See a data description at http://pbil.univ-lyon1.fr/R/pdf/pps027.pdf (in French).

Examples

data(baran95)
w <- dudi.pca(log(baran95$fau + 1), scal = FALSE, scann = FALSE, 
    nf = 3)
w1 <- wca(w, baran95$plan$date, scann = FALSE)
fatala <- ktab.within(w1)
stat1 <- statis(fatala, scan = FALSE, nf = 3)
mfa1 <- mfa(fatala, scan = FALSE, nf = 3)

if(adegraphicsLoaded()) {
  g1 <- s.class(stat1$C.Co, baran95$plan$site, facets = baran95$plan$date, 
    pellipses.axes.draw = FALSE, ppoints.cex = 0.5, plot = FALSE)
  n1 <- length(g1@ADEglist)
  g2 <- ADEgS(lapply(1:n1, function(i) s.label(stat1$C.Co, plabels.cex = 0, 
    ppoints.cex = 0.5, plot = FALSE)), positions = g1@positions, plot = FALSE)
  G1 <- superpose(g2, g1, plot = TRUE)
    
  G2 <- kplot(stat1, arrow = FALSE, traject = FALSE, class = baran95$plan$site, 
    col.plabels.cex = 0, ppoints.cex = 0.5)
  
  g3 <- s.class(mfa1$co, baran95$plan$site, facets = baran95$plan$date, 
    pellipses.axes.draw = FALSE, ppoints.cex = 0.5, plot = FALSE)
  n2 <- length(g3@ADEglist)
  g4 <- ADEgS(lapply(1:n2, function(i) s.label(mfa1$co, plabels.cex = 0, 
    ppoints.cex = 0.5, plot = FALSE)), positions = g3@positions, plot = FALSE)
  G3 <- superpose(g4, g3, plot = TRUE)
    
} else {
  par(mfrow = c(3, 2))
  w2 <- split(stat1$C.Co, baran95$plan$date)
  w3 <- split(baran95$plan$site, baran95$plan$date)
  for (j in 1:6) {
    s.label(stat1$C.Co[,1:2], clab = 0, sub = tab.names(fatala)[j], csub = 3)
    s.class(w2[[j]][, 1:2], w3[[j]], clab = 2, axese = FALSE, add.plot = TRUE)
  }
  par(mfrow = c(1, 1))
  
  kplot(stat1, arrow = FALSE, traj = FALSE, clab = 2, uni = TRUE, 
    class = baran95$plan$site) #simpler
    
  par(mfrow = c(3, 2))
  w4 <- split(mfa1$co, baran95$plan$date)
  for (j in 1:6) {
    s.label(mfa1$co[, 1:2], clab = 0, sub = tab.names(fatala)[j], csub = 3)
    s.class(w4[[j]][, 1:2], w3[[j]], clab = 2, axese = FALSE, add.plot = TRUE)
  }
  par(mfrow = c(1, 1))
}