paper.md

In richelbilderbeek/aureole: R interface to the Encyclopedia of Life

title: 'aureole: use the Encyclopedia of Life' tags: - R - database access authors: - name: Richèl J.C. Bilderbeek orcid: 0000-0003-1107-7049 affiliation: 1 affiliations: - name: Theoretical & Evolutionary Community Ecology, TRES, GELIFES, University of Groningen index: 1 date: 23 February 2020 bibliography: paper.bib

Example text below

Summary

The Encyclopedia of Life [@Wilson:2003] tries to document all living species. This ambitious process has already been cited more than 450 times.

aureole allows access to the Encyclopedia of Life from R.

aureole logo

mcbette is an R package that helps to pick the 'best' model. The 'best', in this context, is the model that is 'simple enough, but not simpler'. In more precise term, mcbette does a model comparison (hence the mc in its name) between multiple suggested evolutionary models and shows which one is best. The winner of this comparison is assumed to result in the best phylogenies (with the same definition of 'best').

To connect to this wealth of information from R, the reol package [@Banbury:2014] was developed and put on CRAN. Due to lack of maintanance, reol was removed from CRAN.

mcbette is aimed to be used by anyone interested in phylogenetics. mcbette builds heavily upon the babette R package [@Bilderbeek:2018], where babette is an R package to call the phylogenetic tool 'BEAST2' [@Bouckaert:2019]. Additionally, mcbette uses the novel 'NS' 'BEAST2' package [@Russel:2019] to do the actual model comparison. With mcbette it will be 'as easy as possible, but not easier' to pick a best evolutionary model.

References

• @Wilson:2003: Wilson, Edward O. "The encyclopedia of life." Trends in Ecology & Evolution 18.2 (2003): 77-80.
• @Banbury:2014: Banbury, Barbara L., and Brian C. O'Meara. "Reol: R interface to the E ncyclopedia of L ife." Ecology and Evolution 4.12 (2014): 2577-2583.

richelbilderbeek/aureole documentation built on March 4, 2020, 10:47 p.m.