R: Genetics-Ecology-Environment Triple

butterfly {ade4} | R Documentation

## 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))
    }

[Package ade4 version 1.7-18 Index]