# Population Structure Model Inference and Visualisation

## Documentation for package ‘starmie’ version 0.1.2

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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