R: Small Ecological Dataset

atlas {ade4} | R Documentation

## Small Ecological Dataset

### Description

`atlas` is a list containing three kinds of information about 23 regions (The French Alps) :
geographical coordinates, meteorology and bird presences.

### Usage

    data(atlas)

### Format

`atlas` is a list of 9 components:

area

  is a convex hull of 23 geographical regions.

xy

  are the coordinates of the region centers and altitude (in meters).

names.district

  is a vector of region names.

meteo

  is a data frame with 7 variables: min and max temperature in january; min and max temperature in july; january, july and total rainfalls.

birds

  is a data frame with 15 variables (species).

contour

  is a data frame with 4 variables (x1, y1, x2, y2) for the contour display of The French Alps.

alti

  is a data frame with 3 variables altitude in percentage [0,800], ]800,1500] and ]1500,5000].

Spatial

  is the map of the 23 regions of The French Alps (an object of the class `SpatialPolygons` of `sp`).

Spatial.contour

  is the contour of the map of the 23 regions of the French Alps (an object of the class `SpatialPolygons` of `sp`).

### Source

Extract from:
Lebreton, Ph. (1977) Les oiseaux nicheurs rhonalpins. Atlas ornithologique Rhone-Alpes. Centre Ornithologique Rhone-Alpes, Universite Lyon 1, 69621 Villeurbanne. Direction de la Protection de la Nature, Ministere de la Qualite de la Vie. 1–354.

### Examples

    data(atlas)
    if(adegraphicsLoaded()) {
      if(requireNamespace("sp", quietly = TRUE)) {
        g11 <- s.Spatial(atlas$Spatial, pSp.col = "white", plot = FALSE)
        g12 <- s.label(atlas$area[, 2:3], plabels.cex = 0, plot = FALSE)
        g1 <- superpose(g11, g12, plot = FALSE)
        g2 <- s.label(atlas$xy, lab = atlas$names.district, Sp = atlas$Spatial,
          pgrid.dra = FALSE, pSp.col = "white", plot = FALSE)
        obj3 <- sp::SpatialPolygonsDataFrame(Sr = atlas$Spatial, data = atlas$meteo)
        g3 <- s.Spatial(obj3[, 1], nclass = 12, psub = list(position = "topleft",
          text = "Temp Mini January", cex = 2), plot = FALSE)
        g4 <- s.corcircle((dudi.pca(atlas$meteo, scann = FALSE)$co), plabels.cex = 1, plot = FALSE)
        G1 <- ADEgS(list(g1, g2, g3, g4), layout = c(2, 2))

        obj5 <- sp::SpatialPolygonsDataFrame(Sr = atlas$Spatial,
          data = dudi.pca(atlas$meteo, scann = FALSE)$li)
        g5 <- s.Spatial(obj5[, 1], nclass = 12, psub = list(position = "topleft",
          text = "Principal Component Analysis analysis", cex = 1.5), plot = FALSE)
        coa1 <- dudi.coa(atlas$birds, scann = FALSE, nf = 1)
        obj6 <- sp::SpatialPolygonsDataFrame(Sr = atlas$Spatial, data = coa1$li)
        g6 <- s.Spatial(obj6[, 1], nclass = 12, psub = list(position = "topleft",
          text = "Correspondence analysis", cex = 1.5), plot = FALSE)
        g7 <- s.value(atlas$xy, coa1$li$Axis1, Sp = atlas$Spatial.contour, ppoints.cex = 2,
          porigin.include = FALSE, paxes.draw = FALSE, pSp.col = "white", plot = FALSE)
        g8 <- triangle.label(atlas$alti, plabels.cex = 0, plot = FALSE)
        G2 <- ADEgS(list(g5, g6, g7, g8), layout = c(2, 2))

      }
    } else {
      op <- par(no.readonly = TRUE)
      par(mfrow = c(2, 2))
      area.plot(atlas$area, cpoin = 1.5)
      area.plot(atlas$area, lab = atlas$names.district, clab = 1)
      x <- atlas$meteo$mini.jan

      names(x) <- row.names(atlas$meteo)
      area.plot(atlas$area, val = x, ncl = 12, sub = "Temp Mini January", csub = 2, cleg = 1)
      s.corcircle((dudi.pca(atlas$meteo, scann = FALSE)$co), clab = 1)

      area.plot(atlas$area, val = dudi.pca(atlas$meteo,scann=FALSE)$li[, 1], ncl = 12,
        sub = "Principal Component Analysis analysis", csub = 1.5, cleg = 1)
      birds.coa <- dudi.coa(atlas$birds, sca = FALSE, nf = 1)
      x <- birds.coa$li$Axis1
      area.plot(atlas$area, val = x, ncl = 12, sub = "Correspondence analysis", csub = 1.5, cleg = 1)

      s.value(atlas$xy, x, contour = atlas$contour, csi = 2, incl = FALSE, addax = FALSE)
      triangle.plot(atlas$alti)
      par(op)
      par(mfrow = c(1, 1))}

[Package ade4 version 1.7-15 Index]