ade4: butterfly – R documentation

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butterfly

Genetics-Ecology-Environment Triple

Description

This data set contains environmental and genetics informations about 16 Euphydryas editha butterfly colonies studied in California and Oregon.

Usage

data(butterfly)

Format

butterfly is a list with the following components:

xy: a data frame with the two coordinates of the 16 Euphydryas editha butterfly colonies
envir: a environmental data frame of 16 sites - 4 variables
genet: a genetics data frame of 16 sites - 6 allele frequencies
contour: a data frame for background map (California map)
Spatial: an object of the class SpatialPolygons of sp, containing the map

Source

McKechnie, S.W., Ehrlich, P.R. and White, R.R. (1975). Population genetics of Euphydryas butterflies. I. Genetic variation and the neutrality hypothesis. Genetics, 81, 571–594.

References

Manly, B.F. (1994) Multivariate Statistical Methods. A primer. Second edition. Chapman & Hall, London. 1–215.

Examples

data(butterfly)

if(adegraphicsLoaded()) {
  if(requireNamespace("sp", quietly = TRUE)) {
    g1 <- s.label(butterfly$xy, Sp = butterfly$Spatial, pSp.col = "white", 
      porigin.include = FALSE, plot = FALSE)
    g2 <- table.value(dist(butterfly$xy), plot = FALSE)
    g3 <- s.value(butterfly$xy, dudi.pca(butterfly$envir, scan = FALSE)$li[, 1], 
      Sp = butterfly$Spatial, pori.inc = FALSE, pSp.col = "transparent", ppoints.cex = 2, 
        plot = FALSE)
    ## mt <- mantel.randtest(dist(butterfly$xy), dist(butterfly$gen), 99)
    G <- ADEgS(list(g1, g2, g3), layout = c(2, 2), plot = TRUE)
  }
} else {
  par(mfrow = c(2, 2))
  s.label(butterfly$xy, contour = butterfly$contour, inc = FALSE)
  table.dist(dist(butterfly$xy), labels = row.names(butterfly$xy)) # depends of mva
  s.value(butterfly$xy, dudi.pca(butterfly$envir, scan = FALSE)$li[,1], 
      contour = butterfly$contour, inc = FALSE, csi = 3)
  plot(mantel.randtest(dist(butterfly$xy), dist(butterfly$gen), 99),
      main = "genetic/spatial")
  par(mfrow = c(1,1))
}

ade4

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

v1.7-16

GPL (>= 2)

Authors

Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.

Initial release