setup_tmb

Sets up executable for the .cpp file (tpl) by looking for exe in package directory or
compiles cpp file in local directory (clean=FALSE) of from package directory.

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_tmb function

<dl><dt>tpl</dt>
<dd>character string for admb template file</dd>
<dt>clean</dt>
<dd>if TRUE, deletes the tpl (.cpp) and executable files in local directory and copies from package directory</dd>
<dt>debug</dt>
<dd>if TRUE, writes out debug line values in code</dd></dl>

Arguments

TMB setup — setup_tmb

<dl>

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


<dt>clean</dt>
<dd>if TRUE, deletes the tpl (.cpp) and executable files in local directory and copies from package directory</dd>


<dt>debug</dt>
<dd>if TRUE, writes out debug line values in code</dd>

</dl>

setup_tmb: TMB setup

Description

Usage

Arguments