RPANDA-package: RPANDA

In hmorlon/PANDA: Phylogenetic ANalyses of DiversificAtion

RPANDA

Description

Implements macroevolutionary analyses on phylogenetic trees

Details

More information on the RPANDA package and worked examples can be found in Morlon et al. (2016)

Author(s)

Hélène Morlon <[e-mail]>

Julien Clavel <[e-mail]>

Fabien Condamine <[e-mail]>

Jonathan Drury <[e-mail]>

Eric Lewitus <[e-mail]>

Marc Manceau <[e-mail]>

Olivier Billaud <[e-mail]>

Odile Maliet <[e-mail]>

Leandro Aristide <[e-mail]>

Benoît Perez-Lamarque <[e-mail]>

References

Morlon, H., Potts, M.D., Plotkin, J.B. (2010) Inferring the dynamics of diversification: a coalescent approach, PLoS B 8(9): e1000493

Morlon, H., Parsons, T.L. and Plotkin, J.B. (2011) Reconciling molecular phylogenies with the fossil record, Proc Nat Acad Sci 108: 16327-16332

Morlon, H., Kemps, B., Plotkin, J.B., Brisson, D. (2012) Explosive radiation of a bacterial species group, Evolution 66: 2577-2586

Condamine, F.L., Rolland, J., and Morlon, H. (2013) Macroevolutionary perspectives to environmental change, Eco Lett 16: 72-85

Morlon, H. (2014) Phylogenetic approaches for studying diversification, Eco Lett 7: 508-525

Manceau, M., Lambert, A., Morlon, H. (2015) Phylogenies support out-of-equilibrium models of biodiversity, Eco Lett 18: 347-356

Lewitus, E., Morlon, H. (2016) Characterizing and comparing phylogenies from their Laplacian spectrum, Syst Biol 65: 495-507

Morlon, H., Lewitus, E., Condamine, F.L., Manceau, M., Clavel, J., Drury, J. (2016) RPANDA: an R package for macroevolutionary analyses on phylogenetic trees, MEE 7: 589-597

Drury, J., Clavel, J., Manceau, M., Morlon, H. (2016) Estimating the Effect of Competition on Trait Evolution Using Maximum Likelihood Inference, Syst Biol 65: 700-710

Manceau, M., Lambert, A., Morlon, H. (2017) A Unifying Comparative Phylogenetic Framework Including Traits Coevolving Across Interacting Lineages, Syst Biol 66: 551-568

Clavel, J., Morlon, H. (2017) Accelerated body size evolution during cold climatic periods in the Cenozoic, Proc Nat Acad Sci 114: 4183-4188

Drury, J., Tobias, J., Burns, K., Mason, N., Shultz, A., and Morlon, H. (2018) Contrasting impacts of competition on ecological and social trait evolution in songbirds. PLOS Biolog 16: e2003563

Clavel, J., Aristide, L., Morlon, H. (2019). A Penalized Likelihood framework for high-dimensional phylogenetic comparative methods and an application to new-world monkeys brain evolution. Syst Biol 68: 93-116

Maliet, O., Hartig, F., Morlon, H. (2019). A model with many small shifts for estimating species-specific diversification rates. Nature Ecol Evol 3: 1086-1092

Condamine, F.L., Rolland, J., Morlon, H. (2019) Assessing the causes of diversification slowdowns: temperature-dependent and diversity-dependent models receive equivalent support Ecology Letters 22: 1900-1912

Aristide, L., Morlon, H. (2019) Understanding the effect of competition during evolutionary radiations: an integrated model of phenotypic and species diversification Ecology Letters 22: 2006-2017

Billaud, O., Moen, D. S., Parsons, T. L., Morlon, H. (2019) Estimating Diversity Through Time using Molecular Phylogenies: Old and Species-Poor Frog Families are the Remnants of a Diverse Past Systematic Biology 69: 363–383

Lewitus, E., Aristide, L., Morlon, H. (2019) Characterizing and Comparing Phylogenetic Trait Data from Their Normalized Laplacian Spectrum Systematic Biology 69: 234–248

Maliet, O., Loeuille, N., Morlon, H. (2020) An individual-based model for the eco-evolutionary emergence of bipartite interaction networks Ecology Letters

Perez-Lamarque, B., Öpik, M., Maliet, O., Afonso Silva, A.C., Selosse, M-A., Martos, F., Morlon, H. (2022), Analysing diversification dynamics using barcoding data: The case of an obligate mycorrhizal symbiont, Molecular Ecology, 31:3496–512.

Perez-Lamarque, B., Maliet, O., Pichon, B., Selosse, M-A., Martos, F., Morlon, H. (2022) Do closely related species interact with similar partners? Testing for phylogenetic signal in bipartite interaction networks. bioRxiv, 2021.08.30.458192, ver. 6 peer-reviewed and recommended by Peer Community in Evolutionary Biology.

hmorlon/PANDA documentation built on April 24, 2024, 3:27 a.m.