setup_admb

Sets up executable for the tpl file by looking for exe in package directory or
compiles tpl file in local directory (clean=F) of from package directory.
If admb cannot be found will attempt to run prepare_admb function (if exists) to
establish connections for compilation.

Functions for fitting various models to capture-recapture data
including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and
the multi-variate state model structure for survival
estimation and POPAN structured Jolly-Seber models for abundance estimation.
There are also Hidden Markov model (HMM) implementations of CJS and multistate
models with and without state uncertainty and a simulation capability for HMM
models.

Jeff Laake

marked

Mark-Recapture Analysis for Survival and Abundance Estimation

setup_admb function

<dl><dt>tpl</dt>
<dd>character string for admb template file</dd>
<dt>compile</dt>
<dd>if TRUE forces re-compilation of tpl file</dd>
<dt>clean</dt>
<dd>if TRUE, deletes the tpl and executable files for amdb in local directory</dd>
<dt>safe</dt>
<dd>can be used to set safe mode for admb</dd>
<dt>re</dt>
<dd>uses admb-re if TRUE for random effects</dd></dl>

Arguments

ADMB setup — setup_admb

<dl>

<dt>tpl</dt>
<dd>character string for admb template file</dd>


<dt>compile</dt>
<dd>if TRUE forces re-compilation of tpl file</dd>


<dt>clean</dt>
<dd>if TRUE, deletes the tpl and executable files for amdb in local directory</dd>


<dt>safe</dt>
<dd>can be used to set safe mode for admb</dd>


<dt>re</dt>
<dd>uses admb-re if TRUE for random effects</dd>

</dl>

setup_admb: ADMB setup

Description

Usage

Arguments