Population Structure Model Inference and Visualisation


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Documentation for package ‘starmie’ version 0.1.2

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admix Constructor for admix object
admixList Contructor for admixList
averagePairWiseSimilarityH Average Q matrices.
averageQ Average Q matrices.
bestK Determine a suitable K value from multiple Structure runs
clumpak Run the CLUMPP algorithms.
clumpp Run the CLUMPP algorithms.
exampleAdmixture Example admixture runs
exampleStructure Example structure objects
getClusterAlleleFreqMat Retrieve estimated within-cluster allele frequencies
getCompleteAlleleFreqMat Retrieve estimated population allele frequencies
getD Accessor methods for struct objects
getFitStats Accessor methods for struct objects
getK Retrieve the assumed number of populations from 'struct' or 'admix' objects.
getMCMC Accessor methods for struct objects
getPosterior Accessor methods for struct objects
getQ Retrieve Q matrix from 'struct' or 'admix' objects.
getStephens Use the Stephen's method to permute sample labels
loadAdmixture Read Admixture Output
loadStructure Read Structure Output
plotBar Generate a barplot of a Structure or Admixture run.
plotMCMC Plot STRUCTURE MCMC chains
plotMDS Plot principal coordinates from Q-matrix, struct or admix objects
plotMultiK Generate a barplot for multiple values of K..
plotTreeBar Generate a barplot of a Structure or Admixture run.
runStructure Run STRUCTURE in current path
struct Constructor for struct object
structList Constructor for a structList object