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AtutorialforDiscriminantAnalysisofPrincipal
Components(DAPC)using
adegenet
2.0.0
ThibautJombart,CaitlinCollins
ImperialCollegeLondon
MRCCentreforOutbreakAnalysisandModelling
June23,2015
Abstract
ThisvignetteprovidesatutorialforapplyingtheDiscriminantAnalysisofPrincipal
Components(DAPC[
1
])usingthe
adegenet
package[
2
]fortheRsoftware[
3
].This
methodsaimstoidentifyanddescribegeneticclusters,althoughitcaninfactbeapplied
toanyquantitativedata.Weillustratehowtouse
find.clusters
toidentifyclusters,
and
dapc
todescribetherelationshipsbetweentheseclusters.Moreadvancedtopics
arethenintroduced,suchasadvancedgraphics,assessingthestabilityofDAPCresults
andusingsupplementaryindividuals.
,
caitlin.collins12@imperial.ac.uk
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