clean_tnrs

Eliminates unmatched (NAs) and invalid taxa from a <code>rotl::tnrs_match_names()</code> or <code>tnrs_match()</code> output
Useful to get ott ids to retrieve an induced synthetic Open Tree of Life.
Needed because using <code>include_suppressed = FALSE</code> in <code>rotl::tnrs_match_names()</code> does not drop all invalid taxa.

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

clean_tnrs function

<dl><dt>tnrs</dt>
<dd>A data frame, usually an output from datelife::tnrs_match or rotl::tnrs_match_names functions, but see details.</dd>
<dt>invalid</dt>
<dd>A character string with flags to be removed from final object.</dd>
<dt>remove_nonmatches</dt>
<dd>Boolean, whether to remove unsuccessfully matched names or not.</dd></dl>

Arguments

Eliminates unmatched (NAs) and invalid taxa from a rotl::tnrs_match_names() or tnrs_match() output
Useful to get ott ids to retrieve an induced synthetic Open Tree of Life.
Needed because using include_suppressed = FALSE in rotl::tnrs_match_names() does not drop all invalid taxa. — clean_tnrs

<dl>

<dt>tnrs</dt>
<dd>A data frame, usually an output from datelife::tnrs_match or rotl::tnrs_match_names functions, but see details.</dd>


<dt>invalid</dt>
<dd>A character string with flags to be removed from final object.</dd>


<dt>remove_nonmatches</dt>
<dd>Boolean, whether to remove unsuccessfully matched names or not.</dd>

</dl>

Eliminates unmatched (NAs) and invalid taxa from a <code>rotl::tnrs_match_names()</code> or <code>tnrs_match()</code> output
Useful to get ott ids to retrieve an induced synthetic Open Tree of Life.
Needed because using <code>include_suppressed = FALSE</code> in <code>rotl::tnrs_match_names()</code> does not drop all invalid taxa.

clean_tnrs: Eliminates unmatched (NAs) and invalid taxa from a `rotl::tnrs_match_names()` or `tnrs_match()` output Useful to get ott ids to retrieve an induced synthetic Open Tree of Life. Needed because using `include_suppressed = FALSE` in `rotl::tnrs_match_names()` does not drop all invalid taxa.

Description

Usage

Value

Arguments

Details