self_assign

Implements Bayesian inference for the conditional genetic
stock identification model. It allows inference of mixed fisheries and also
simulation of mixtures to predict accuracy. A full description of the underlying
methods is available in a recently published article in the
Canadian Journal of Fisheries and Aquatic Sciences: <doi:10.1139/cjfas-2018-0016>.

Eric C. Anderson

rubias

Bayesian Inference from the Conditional Genetic Stock
Identification Model

self_assign function

<dl><dt>reference</dt>
<dd>a two-column format genetic dataset, with "repunit", "collection", and "indiv"
columns, as well as a "sample_type" column that has some "reference" entries</dd>
<dt>gen_start_col</dt>
<dd>the first column of genetic data in <code>reference</code></dd>
<dt>preCompiledParams</dt>
<dd>Users should never use this option. It is here only so that
this function can be called on a precompiled set of parameters with infer_mixture. Don't
use this, unless you are one of the package developers...</dd>
<dt>alle_freq_prior</dt>
<dd>a one-element named list specifying the prior to be used when
generating Dirichlet parameters for genotype likelihood calculations. Valid methods include
<code>"const"</code>, <code>"scaled_const"</code>, and <code>"empirical"</code>. See <code>?list_diploid_params</code>
for method details.</dd></dl>

Arguments

Do leave-one-out self-assignment of individuals in a reference baseline — self_assign

<dl>

<dt>reference</dt>
<dd>a two-column format genetic dataset, with "repunit", "collection", and "indiv"
columns, as well as a "sample_type" column that has some "reference" entries</dd>


<dt>gen_start_col</dt>
<dd>the first column of genetic data in <code>reference</code></dd>


<dt>preCompiledParams</dt>
<dd>Users should never use this option. It is here only so that
this function can be called on a precompiled set of parameters with infer_mixture. Don't
use this, unless you are one of the package developers...</dd>


<dt>alle_freq_prior</dt>
<dd>a one-element named list specifying the prior to be used when
generating Dirichlet parameters for genotype likelihood calculations. Valid methods include
<code>"const"</code>, <code>"scaled_const"</code>, and <code>"empirical"</code>. See <code>?list_diploid_params</code>
for method details.</dd>

</dl>

self_assign: Do leave-one-out self-assignment of individuals in a reference baseline

Description

Usage

Value

Arguments

Examples