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MODELLING TRAIT-DEPENDENT SPECIATION WITH APPROXIMATE BAYESIAN COMPUTATION
Linköping University, Department of Computer and Information Science, The Division of Statistics and Machine Learning. Linköping University, Faculty of Arts and Sciences.ORCID iD: 0000-0002-5816-4345
Univ Cambridge, England.
2019 (English)In: ACTA PHYSICA POLONICA B PROCEEDINGS SUPPLEMENT, JAGIELLONIAN UNIV , 2019, Vol. 12, no 1, p. 25-47Conference paper, Published paper (Refereed)
Abstract [en]

Phylogeny is the field of modelling the temporal discrete dynamics of speciation. Complex models can nowadays be studied using the Approximate Bayesian Computation approach which avoids likelihood calculations. The fields progression is hampered by the lack of robust software to estimate the numerous parameters of the speciation process. In this work, we present an R package, pcmabc, publicly available on CRAN, based on Approximate Bayesian Computations, that implements three novel phylogenetic algorithms for trait-dependent speciation modelling. Our phylogenetic comparative methodology takes into account both the simulated traits and phylogeny, attempting to estimate the parameters of the processes generating the phenotype and the trait. The user is not restricted to a predefined set of models and can specify a variety of evolutionary and branching models. We illustrate the software with a simulation-reestimation study focused around the branching Ornstein-Uhlenbeck process, where the branching rate depends non-linearly on the value of the driving Ornstein-Uhlenbeck process. Included in this work is a tutorial on how to use the software.

Place, publisher, year, edition, pages
JAGIELLONIAN UNIV , 2019. Vol. 12, no 1, p. 25-47
National Category
Probability Theory and Statistics
Identifiers
URN: urn:nbn:se:liu:diva-159603DOI: 10.5506/APhysPolBSupp.12.25ISI: 000476897100003OAI: oai:DiVA.org:liu-159603DiVA, id: diva2:1342254
Conference
Summer Solstice International Conference on Discrete Models of Complex Systems
Note

Funding Agencies|Swedish Research Councils (Vetenskapsradet) [2017-04951]

Available from: 2019-08-13 Created: 2019-08-13 Last updated: 2019-09-04

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Bartoszek, Krzysztof
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CiteExportLink to record
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Cite
Citation style
  • apa
  • harvard1
  • ieee
  • modern-language-association-8th-edition
  • vancouver
  • oxford
  • Other style
More styles
Language
  • de-DE
  • en-GB
  • en-US
  • fi-FI
  • nn-NO
  • nn-NB
  • sv-SE
  • Other locale
More languages
Output format
  • html
  • text
  • asciidoc
  • rtf