data.block

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

datasets

A method for modeling genetic data as a combination of discrete
layers, within each of which relatedness may decay continuously with geographic
distance. This package contains code for running analyses (which are implemented
in the modeling language 'rstan') and visualizing and interpreting output. See the
paper for more details on the model and its utility.

Gideon Bradburd

conStruct

Models Spatially Continuous and Discrete Population Genetic
Structure

data.block function

A list with 7 elements:<dl>
	<dt><code>N</code></dt>
<dd>the number of samples included in the analysis</dd>	<dt><code>K</code></dt>
<dd>the number of clusters/layers included in the model</dd>	<dt><code>spatial</code></dt>
<dd>a boolean indicating whether the spatial
		model has been specified</dd>	<dt><code>L</code></dt>
<dd>the number of loci included in the analysis</dd>	<dt><code>coords</code></dt>
<dd>a matrix with one row for each of the <code>N</code> samples, 
		in the same order as that of the <code>obsCov</code> matrix, 
		and two columns, the first giving the x-coordinate 
		(or longitude), the second giving the y-coordinate (or latitude)</dd>	<dt><code>obsCov</code></dt>
<dd>the sample allelic covariance matrix, 
		in the same order as that of the <code>coords</code> matrix, 
		with <code>N</code> rows and columns</dd>	<dt><code>geoDist</code></dt>
<dd>a matrix of pairwise geographic distance between , 
		samples in the same order as that of the <code>obsCov</code>, 
		with <code>N</code> rows and columns</dd>	<dt><code>sd.geoDist</code></dt>
<dd>the standard deviation of the raw geographic 
		distance matrix, used for normalizing <code>geoDist</code> within the 
		stan model</dd>	<dt><code>varMeanFreqs</code></dt>
<dd>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)</dd>
</dl>

Format

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

A list with 7 elements:<dl>
	<dt><code>N</code></dt>
<dd>the number of samples included in the analysis</dd>

	<dt><code>K</code></dt>
<dd>the number of clusters/layers included in the model</dd>

	<dt><code>spatial</code></dt>
<dd>a boolean indicating whether the spatial
		model has been specified</dd>

	<dt><code>L</code></dt>
<dd>the number of loci included in the analysis</dd>

	<dt><code>coords</code></dt>
<dd>a matrix with one row for each of the <code>N</code> samples, 
		in the same order as that of the <code>obsCov</code> matrix, 
		and two columns, the first giving the x-coordinate 
		(or longitude), the second giving the y-coordinate (or latitude)</dd>

	<dt><code>obsCov</code></dt>
<dd>the sample allelic covariance matrix, 
		in the same order as that of the <code>coords</code> matrix, 
		with <code>N</code> rows and columns</dd>

	<dt><code>geoDist</code></dt>
<dd>a matrix of pairwise geographic distance between , 
		samples in the same order as that of the <code>obsCov</code>, 
		with <code>N</code> rows and columns</dd>

	<dt><code>sd.geoDist</code></dt>
<dd>the standard deviation of the raw geographic 
		distance matrix, used for normalizing <code>geoDist</code> within the 
		stan model</dd>

	<dt><code>varMeanFreqs</code></dt>
<dd>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)</dd>


</dl>

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

Description

Usage

Arguments

Format