check_ott_input

<code>check_ott_input is currently used in functions </code><code>get_ott_clade()</code>,
<code>get_ott_children()</code>, and <code>get_otol_synthetic_tree()</code>.

Methods and workflows to get chronograms (i.e., phylogenetic trees with branch lengths
proportional to time), using open, peer-reviewed, state-of-the-art scientific data on time of lineage divergence.
This package constitutes the main underlying code of the DateLife web service
at <https://www.datelife.org>. To obtain a single summary chronogram from a group of
relevant chronograms, we implement the Super Distance Matrix (SDM) method
described in Criscuolo et al. (2006) <doi:10.1080/10635150600969872>.
To find the grove of chronograms with a sufficiently overlapping set of taxa
for summarizing, we implement theorem 1.1. from Ané et al. (2009)
<doi:10.1007/s00026-009-0017-x>.
A given phylogenetic tree can be dated using time of lineage divergence data
as secondary calibrations (with caution, see Schenk (2016) <doi:10.1371/journal.pone.0148228>).
To obtain and apply secondary calibrations, the package implements the congruification method described
in Eastman et al. (2013) <doi:10.1111/2041-210X.12051>. Tree dating can be performed with different methods
including BLADJ (Webb et al. (2008) <doi:10.1093/bioinformatics/btn358>), PATHd8
(Britton et al. (2007) <doi:10.1080/10635150701613783>), mrBayes (Huelsenbeck
and Ronquist (2001) <doi:10.1093/bioinformatics/17.8.754>), and treePL (Smith
and O'Meara (2012) <doi:10.1093/bioinformatics/bts492>).

Luna L. Sanchez Reyes

datelife

Scientific Data on Time of Lineage Divergence for Your Taxa

Brian O'Meara

Jonathan Eastman

Tracy Heath

April Wright

Klaus Schliep

Scott Chamberlain

Peter Midford

Luke Harmon

Joseph Brown

Matt Pennell

Mike Alfaro

Emily Jane McTavish

check_ott_input function

<dl><dt>input</dt>
<dd>Optional. A character vector of names or a <code>datelifeQuery</code> object.</dd>
<dt>ott_ids</dt>
<dd>If not NULL, it takes this argument and ignores input. A
numeric vector of ott ids obtained with <code>rotl::taxonomy_taxon_info()</code> or
<code>rotl::tnrs_match_names()</code> or <code>tnrs_match()</code>.</dd>
<dt>...</dt>
<dd>Arguments passed on to <code>make_datelife_query</code><dl>
 <dt><code>use_tnrs</code></dt>
<dd>Whether to use Open Tree of Life's Taxonomic Name Resolution Service (TNRS)
to process input taxon names. Default to <code>TRUE</code>, it corrects misspellings and
taxonomic name variations with <code>tnrs_match()</code>, a wrapper of <code>rotl::tnrs_match_names()</code>.</dd></dl></dd> <dt><code>get_spp_from_taxon</code></dt>
<dd>Whether to search ages for all species belonging to a
given taxon or not. Default to <code>FALSE</code>. If <code>TRUE</code>, it must have same length as input.
If input is a newick string with some clades it will be converted to a <code>phylo</code>
object, and the order of <code>get_spp_from_taxon</code> will match <code>phy$tip.label</code>.</dd> <dt><code>reference_taxonomy</code></dt>
<dd>A character vector specifying the reference taxonomy to use for TNRS.
Options are "ott", "ncbi", "gbif" or "irmng". The function defaults to "ott".</dd> 
</dl>

Arguments

Check input for usage in other datelife functions — check_ott_input

<dl>

<dt>input</dt>
<dd>Optional. A character vector of names or a <code>datelifeQuery</code> object.</dd>


<dt>ott_ids</dt>
<dd>If not NULL, it takes this argument and ignores input. A
numeric vector of ott ids obtained with <code>rotl::taxonomy_taxon_info()</code> or
<code>rotl::tnrs_match_names()</code> or <code>tnrs_match()</code>.</dd>


<dt>...</dt>
<dd>Arguments passed on to <code>make_datelife_query</code><dl>
 <dt><code>use_tnrs</code></dt>
<dd>Whether to use Open Tree of Life's Taxonomic Name Resolution Service (TNRS)
to process input taxon names. Default to <code>TRUE</code>, it corrects misspellings and
taxonomic name variations with <code>tnrs_match()</code>, a wrapper of <code>rotl::tnrs_match_names()</code>.</dd>

 <dt><code>get_spp_from_taxon</code></dt>
<dd>Whether to search ages for all species belonging to a
given taxon or not. Default to <code>FALSE</code>. If <code>TRUE</code>, it must have same length as input.
If input is a newick string with some clades it will be converted to a <code>phylo</code>
object, and the order of <code>get_spp_from_taxon</code> will match <code>phy$tip.label</code>.</dd>

 <dt><code>reference_taxonomy</code></dt>
<dd>A character vector specifying the reference taxonomy to use for TNRS.
Options are "ott", "ncbi", "gbif" or "irmng". The function defaults to "ott".</dd>

 
</dl></dd>

</dl>

Check input for usage in other <code>datelife</code> functions

check_ott_input: Check input for usage in other `datelife` functions

Description

Usage

Value

Arguments

Details