ade4 (version 1.7-5)

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:

Source

Baran, E. (1995) Dynamique spatio-temporelle des peuplements de Poissons estuariens en Guinée (Afrique de l'Ouest). Thèse de Doctorat, Université de Bretagne Occidentale. Data collected by net fishing sampling in the Fatala river estuary.

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))
}