Simulated data illustrating the DAPC
Datasets illustrating the Discriminant Analysis of Principal Components
(DAPC, Jombart et al. submitted).
dapcIllus is list of 4 components being all genind objects.
These data were simulated using various models using Easypop (2.0.1). The
dapcIllus is a list containing the following genind
objects:
- "a": island model with 6 populations
- "b": hierarchical
island model with 6 populations (3,2,1)
- "c": one-dimensional stepping
stone with 2x6 populations, and a boundary between the two sets of 6
populations
- "d": one-dimensional stepping stone with 24 populations
See "source" for a reference providing simulation details.
Thibaut Jombart t.jombart@imperial.ac.uk
Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. Submitted to BMC genetics.
Jombart, T., Devillard, S. and Balloux, F. Discriminant analysis of principal components: a new method for the analysis of genetically structured populations. Submitted to Genetics.
- dapc: implements the DAPC.
- eHGDP: dataset illustrating the DAPC and
find.clusters.
- H3N2: dataset illustrating the DAPC.
- find.clusters: to identify clusters without prior.
## Not run: data(dapcIllus) attach(dapcIllus) a # this is a genind object, like b, c, and d. ## FINS CLUSTERS EX NIHILO clust.a <- find.clusters(a, n.pca=100, n.clust=6) clust.b <- find.clusters(b, n.pca=100, n.clust=6) clust.c <- find.clusters(c, n.pca=100, n.clust=12) clust.d <- find.clusters(d, n.pca=100, n.clust=24) ## examin outputs names(clust.a) lapply(clust.a, head) ## PERFORM DAPCs dapc.a <- dapc(a, pop=clust.a$grp, n.pca=100, n.da=5) dapc.b <- dapc(b, pop=clust.b$grp, n.pca=100, n.da=5) dapc.c <- dapc(c, pop=clust.c$grp, n.pca=100, n.da=11) dapc.d <- dapc(d, pop=clust.d$grp, n.pca=100, n.da=23) ## LOOK AT ONE RESULT dapc.a summary(dapc.a) ## FORM A LIST OF RESULTS FOR THE 4 DATASETS lres <- list(dapc.a, dapc.b, dapc.c, dapc.d) ## DRAW 4 SCATTERPLOTS par(mfrow=c(2,2)) lapply(lres, scatter) # detach data detach(dapcIllus) ## End(Not run)
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