R: African Estuary Fishes

baran95 {ade4} | R Documentation

## 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.

### 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))
    }

[Package ade4 version 1.7-19 Index]