write_nexus_matrix

Writes out a morphological data file in #NEXUS format.

Measures morphological diversity from discrete character data and
estimates evolutionary tempo on phylogenetic trees. Imports morphological
data from #NEXUS (Maddison et al. (1997) <doi:10.1093/sysbio/46.4.590>)
format with read_nexus_matrix(), and writes to both #NEXUS and TNT format
(Goloboff et al. (2008) <doi:10.1111/j.1096-0031.2008.00217.x>). Main
functions are test_rates(), which implements AIC and likelihood
ratio tests for discrete character rates introduced across Lloyd et al.
(2012) <doi:10.1111/j.1558-5646.2011.01460.x>, Brusatte et al. (2014)
<doi:10.1016/j.cub.2014.08.034>, Close et al. (2015)
<doi:10.1016/j.cub.2015.06.047>, and Lloyd (2016) <doi:10.1111/bij.12746>,
and calculate_morphological_distances(), which implements multiple discrete
character distance metrics from Gower (1971) <doi:10.2307/2528823>, Wills
(1998) <doi:10.1006/bijl.1998.0255>, Lloyd (2016) <doi:10.1111/bij.12746>,
and Hopkins and St John (2018) <doi:10.1098/rspb.2018.1784>. This also
includes the GED correction from Lehmann et al. (2019)
<doi:10.1111/pala.12430>. Multiple functions implement morphospace plots:
plot_chronophylomorphospace() implements Sakamoto and Ruta (2012)
<doi:10.1371/journal.pone.0039752>, plot_morphospace() implements Wills et
al. (1994) <doi:10.1017/S009483730001263X>, plot_changes_on_tree()
implements Wang and Lloyd (2016) <doi:10.1098/rspb.2016.0214>, and
plot_morphospace_stack() implements Foote (1993)
<doi:10.1017/S0094837300015864>. Other functions include
safe_taxonomic_reduction(), which implements Wilkinson (1995)
<doi:10.1093/sysbio/44.4.501>, map_dollo_changes() implements
the Dollo stochastic character mapping of Tarver et al. (2018)
<doi:10.1093/gbe/evy096>, and estimate_ancestral_states() implements
the ancestral state options of Lloyd (2018) <doi:10.1111/pala.12380>.
calculate_tree_length() and reconstruct_ancestral_states() implements
the generalised algorithms from Swofford and Maddison (1992; no doi).

Graeme T. Lloyd

Claddis

Measuring Morphological Diversity and Evolutionary Tempo

Thomas Guillerme

Jen Hoyal Cuthill

Emma Sherratt

Steve C. Wang

write_nexus_matrix function

<dl><dt>cladistic_matrix</dt>
<dd>The cladistic matrix in the format imported by read_nexus_matrix.</dd>
<dt>file_name</dt>
<dd>The file name to write to. Should end in <code>.nex</code>.</dd></dl>

Arguments

Graeme T. Lloyd <a href="/link/graemetlloyd%40gmail.com?package=Claddis&version=0.7.0" data-mini-rdoc="Claddis::graemetlloyd@gmail.com">graemetlloyd@gmail.com</a>

Author

Writes out a morphological #NEXUS data file — write_nexus_matrix

<dl>

<dt>cladistic_matrix</dt>
<dd>The cladistic matrix in the format imported by read_nexus_matrix.</dd>


<dt>file_name</dt>
<dd>The file name to write to. Should end in <code>.nex</code>.</dd>

</dl>

Graeme T. Lloyd <a href='mailto:graemetlloyd@gmail.com'>graemetlloyd@gmail.com</a>

write_nexus_matrix: Writes out a morphological #NEXUS data file

Description

Usage

Arguments

Author

Details

References

See Also

Examples