data.block: Example 'data.block' generated by a 'conStruct' analysis
In conStruct: Models Spatially Continuous and Discrete Population Genetic Structure

data.block

R Documentation

Example `data.block` generated by a `conStruct` analysis

Description

An example data.block object generated in a conStruct analysis from the raw data supplied by the user. This object is automatically saved and is used in several subsequent plotting functions.

Usage

data.block

Format

A list with 7 elements:

N: the number of samples included in the analysis
K: the number of clusters/layers included in the model
spatial: a boolean indicating whether the spatial model has been specified
L: the number of loci included in the analysis
coords: a matrix with one row for each of the N samples, in the same order as that of the obsCov matrix, and two columns, the first giving the x-coordinate (or longitude), the second giving the y-coordinate (or latitude)
obsCov: the sample allelic covariance matrix, in the same order as that of the coords matrix, with N rows and columns
geoDist: a matrix of pairwise geographic distance between , samples in the same order as that of the obsCov, with N rows and columns
sd.geoDist: the standard deviation of the raw geographic distance matrix, used for normalizing geoDist within the stan model
varMeanFreqs: the variance of the mean allele frequencies, averaged over choice of counted allele (passed to the model as a prior on the global covariance parameter)