update_babette

Update all babette dependencies, by installing their
latest versions

'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'.
'babette' provides for an alternative workflow of using
all these tools separately. This allows doing complex Bayesian
phylogenetics easily and reproducibly from 'R'.

Richel Bilderbeek

babette

Control 'BEAST2'

Richèl J.C. Bilderbeek

Joëlle Barido-Sottani

David Winter

Jason Griffiths

Giovanni Laudanno

update_babette function

<dl><dt>upgrade</dt>
<dd>Should package dependencies be upgraded? One of "default", "ask", "always", or "never". "default"
respects the value of the <code>R_REMOTES_UPGRADE</code> environment variable if set,
and falls back to "ask" if unset. "ask" prompts the user for which out of
date packages to upgrade. For non-interactive sessions "ask" is equivalent
to "always". <code>TRUE</code> and <code>FALSE</code> are also accepted and correspond to
"always" and "never" respectively.</dd></dl>

Arguments

Giovanni Laudanno, Richèl J.C. Bilderbeek

Author

Update all babette dependencies, by installing their
latest versions — update_babette

<dl>

<dt>upgrade</dt>
<dd>Should package dependencies be upgraded? One of "default", "ask", "always", or "never". "default"
respects the value of the <code>R_REMOTES_UPGRADE</code> environment variable if set,
and falls back to "ask" if unset. "ask" prompts the user for which out of
date packages to upgrade. For non-interactive sessions "ask" is equivalent
to "always". <code>TRUE</code> and <code>FALSE</code> are also accepted and correspond to
"always" and "never" respectively.</dd>

</dl>

update_babette: Update all babette dependencies, by installing their latest versions

Description

Usage

Arguments

Author

Examples