sdm_spec_boost_tree

This function returns a <a href="https://parsnip.tidymodels.org/reference/model_spec.html">parsnip::model_spec</a> for a Boosted Trees model to be
used as a classifier of presences and absences in Species Distribution Model.
It uses the library <code>xgboost</code> to fit boosted trees; to use another library,
simply build the <a href="https://parsnip.tidymodels.org/reference/model_spec.html">parsnip::model_spec</a> directly.

Fit species distribution models (SDMs) using the 'tidymodels' framework,
which provides a standardised interface to define models and process their
outputs. 'tidysdm' expands 'tidymodels' by providing methods for spatial objects,
models and metrics specific to SDMs,
as well as a number of specialised functions to process occurrences
for contemporary and palaeo datasets. The full
functionalities of the package are described
in Leonardi et al. (2023) <doi:10.1101/2023.07.24.550358>.

Andrea Manica

tidysdm

Species Distribution Models with Tidymodels

Michela Leonardi

Margherita Colucci

Andrea Vittorio Pozzi

Eleanor M.L. Scerri

Ben Tupper

sdm_spec_boost_tree function

<dl><dt>...</dt>
<dd>parameters to be passed to <code><a href="https://parsnip.tidymodels.org/reference/boost_tree.html">parsnip::boost_tree()</a></code> to customise
the model. See the help of that function for details.</dd>
<dt>tune</dt>
<dd>character defining the tuning strategy. Valid strategies are:<ul>
<li>"sdm" chooses hyperparameters that are most important to tune for
an sdm (for boost_tree: 'mtry', 'trees', 'tree_depth', 'learn_rate',
'loss_reduction', and 'stop_iter')</li>
<li>"all" tunes all hyperparameters (for boost_tree: 'mtry', 'trees',
'tree_depth', 'learn_rate', 'loss_reduction', 'stop_iter','min_n' and
'sample_size')</li>
<li>"custom" passes the options from '...'</li>
<li>"none" does not tune any hyperparameter</li>
</ul></dd></dl>

Arguments

This function returns a <a href='https://parsnip.tidymodels.org/reference/model_spec.html'>parsnip::model_spec</a> for a Boosted Trees model to be
used as a classifier of presences and absences in Species Distribution Model.
It uses the library <code>xgboost</code> to fit boosted trees; to use another library,
simply build the <a href='https://parsnip.tidymodels.org/reference/model_spec.html'>parsnip::model_spec</a> directly.

Model specification for a Boosted Trees model for SDM — sdm_spec_boost_tree

<dl>

<dt>...</dt>
<dd>parameters to be passed to <code><a href='https://parsnip.tidymodels.org/reference/boost_tree.html'>parsnip::boost_tree()</a></code> to customise
the model. See the help of that function for details.</dd>


<dt>tune</dt>
<dd>character defining the tuning strategy. Valid strategies are:<ul>
<li>"sdm" chooses hyperparameters that are most important to tune for
an sdm (for boost_tree: 'mtry', 'trees', 'tree_depth', 'learn_rate',
'loss_reduction', and 'stop_iter')</li>
<li>"all" tunes all hyperparameters (for boost_tree: 'mtry', 'trees',
'tree_depth', 'learn_rate', 'loss_reduction', 'stop_iter','min_n' and
'sample_size')</li>
<li>"custom" passes the options from '...'</li>
<li>"none" does not tune any hyperparameter</li>
</ul></dd>

</dl>

sdm_spec_boost_tree: Model specification for a Boosted Trees model for SDM

Description

Usage

Value

Arguments

See Also

Examples