batchLL

batchLL function provides the batch marking log-likelihood

A system for batch-marking data analysis to estimate survival probabilities, capture probabilities, and enumerate the population abundance for both marked and unmarked individuals. The estimation of only marked individuals can be achieved through the batchMarkOptim() function. Similarly, the combined marked and unmarked can be achieved through the batchMarkUnmarkOptim() function. The algorithm was also implemented for the hidden Markov model encapsulated in batchMarkUnmarkOptim() to estimate the abundance of both marked and unmarked individuals in the population. The package is based on the paper: "Hidden Markov Models for Extended Batch Data" of Cowen et al. (2017) <doi:10.1111/biom.12701>.

Kehinde Olobatuyi

extBatchMarking

Extended Batch Marking Models

Simon Johns

Matthew RP Parker

Steve Hof

Laura LE Cowen

batchLL function

<dl><dt>phi</dt>
<dd>The probability of surviving and remaining in the population between occasions t and t +1, given an individual was alive and in the population at occasion t. This must be a number between 0 and 1.</dd>
<dt>p</dt>
<dd>The probability of capture at occasion t. This must be a number between 0 and 1.</dd>
<dt>R</dt>
<dd>The number of individuals marked and released at sampling occasion g from batch group g; g = 1,2,...,G. This must be an integer.</dd>
<dt>begin_g</dt>
<dd>The beginning of the occasion.</dd>
<dt>end_g</dt>
<dd>The end of the occasion.</dd></dl>

Arguments

batchLL function provides the batch marking log-likelihood — batchLL

<dl>

<dt>phi</dt>
<dd>The probability of surviving and remaining in the population between occasions t and t +1, given an individual was alive and in the population at occasion t. This must be a number between 0 and 1.</dd>


<dt>p</dt>
<dd>The probability of capture at occasion t. This must be a number between 0 and 1.</dd>


<dt>R</dt>
<dd>The number of individuals marked and released at sampling occasion g from batch group g; g = 1,2,...,G. This must be an integer.</dd>


<dt>begin_g</dt>
<dd>The beginning of the occasion.</dd>


<dt>end_g</dt>
<dd>The end of the occasion.</dd>

</dl>

batchLL: batchLL function provides the batch marking log-likelihood

Description

Usage

Value

Arguments