butterfly: Genetics-Ecology-Environment Triple

In ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

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 4 components.

xy

is a data frame with the two coordinates of the 16 Euphydryas editha butterfly colonies.

envir

is a environmental data frame of 16 sites - 4 variables.

genet

is a genetics data frame of 16 sites - 6 allele frequencies.

contour

is a data frame for background map (California 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", quiet = 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$Spatial, pori.inc = FALSE, pSp.col = "transparent", ppoints.cex = 2, plot = F)
##    mt <- mantel.randtest(dist(butterfly$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 documentation built on May 2, 2019, 5:50 p.m.