# Inapplicable data in morphological phylogenetics

#### 2020-07-09

TreeSearch is an R package that allows, among other things, parsimony search on morphological datasets that contain inapplicable data, following the algorithm proposed by Brazeau, Guillerme and Smith (2019).

In brief, this algorithm modifies the Fitch algorithm to count the total number of homoplasious events on a tree.

## Getting started

A companion vignette gives details on installing the package and getting up and running.

Once installed, load the TreeSearch package into R using

library('TreeSearch')

## Implied weighting

Equal weights produces trees that are less accurate and less precise than implied weights (Smith, 2019); equally weighted analysis should never be conducted without also considering the results of implied weights (Goloboff, 1997), ideally under a range of concavity constants (cf. Smith & Ortega-Hernández, 2014).

The simplest way to conduct an implied weights search is to use the functions

IWTreeSearch
IWRatchet
IWMultiRatchet

which operate in the same fashion as their equally-weighted counterparts, with the option of specifying a concavity constant (k) using the parameter concavity=k (default = 10). Note that the default value of 10 is somewhat higher than the default of 3 in TNT; this low default probably gives poorer results in many settings (Smith, 2019).

## References

Brazeau, M. D., Guillerme, T., & Smith, M. R. (2019). An algorithm for morphological phylogenetic analysis with inapplicable data. Systematic Biology, 68(4), 619–631. doi:10.1093/sysbio/syy083

Goloboff, P. A. (1997). Self-weighted optimization: tree searches and character state reconstructions under implied transformation costs. Cladistics, 13(3), 225–245. Retrieved from http://dx.doi.org/10.1111/j.1096-0031.1997.tb00317.x

Nixon, K. C. (1999). The Parsimony Ratchet, a new method for rapid parsimony analysis. Cladistics, 15(4), 407–414. doi:10.1111/j.1096-0031.1999.tb00277.x

Smith, M. R. (2019). Bayesian and parsimony approaches reconstruct informative trees from simulated morphological datasets. Biology Letters, 15(2), 20180632. doi:10.1098/rsbl.2018.0632

Smith, M. R., & Ortega-Hernández, J. (2014). Hallucigenia’s onychophoran-like claws and the case for Tactopoda. Nature, 514(7522), 363–366. doi:10.1038/nature13576

Vinther, J., Van Roy, P., & Briggs, D. E. G. (2008). Machaeridians are Palaeozoic armoured annelids. Nature, 451(7175), 185–188. doi:10.1038/nature06474