To cite RRphylo implementations and auxilliary functions in publications use:

RRphylo package, search.shift, and auxilliary functions

Castiglione S, Tesone G, Piccolo M, Melchionna M, Mondanaro A, Serio C, Febbraro MD, Raia P (2018). “A new method for testing evolutionary rate variation and shifts in phenotypic evolution.” Methods in Ecology and Evolution, 9, 974-983. https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12954.

multiple regression version of RRphylo

Serio C, Castiglione S, Tesone G, Piccolo M, Melchionna M, Mondanaro A, Febbraro MD, Raia P (2019). “Macroevolution of toothed whales exceptional relative brain size.” Evolutionary Biology, 46, 332-342. https://link.springer.com/article/10.1007/s11692-019-09485-7.

Melchionna M, Mondanaro A, Serio C, Castiglione S, Febbraro MD, Rook L, Diniz-Filho JA, Manzi G, Profico A, Sansalone G, Raia P (2020). “Macroevolutionary trends of brain mass in Primates.” Biological Journal of the Linnean Society. https://academic.oup.com/biolinnean/advance-article/doi/10.1093/biolinnean/blz161/5614248.

Ancestral state integration in RRphylo (RRphylo-noder)

Castiglione S, Serio C, Mondanaro A, Melchionna M, Carotenuto F, Febbraro MD, Profico A, Tamagnini D, Raia P (2020). “Ancestral State Estimation with Phylogenetic Ridge Regression.” Evolutionary Biology, 47, 220-232. https://link.springer.com/article/10.1007/s11692-020-09505-x.

search.trend

Castiglione S, Serio C, Mondanaro A, Febbraro MD, Profico A, Girardi G, Raia P (2019). “Simultaneous detection of macroevolutionary patterns in phenotypic means and rate of change with and within phylogenetic trees including extinct species.” PLoS ONE, 14, e0210101. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210101.

search.conv

Castiglione S, Serio C, Tamagnini D, Melchionna M, Mondanaro A, Febbraro MD, Profico A, Piras P, Barattolo F, Raia P (2019). “A new, fast method to search for morphological convergence with shape data.” PLoS ONE, 14, e0226949. https://doi.org/10.1371/journal.pone.0226949.

fix.poly

Castiglione S, Serio C, Piccolo M, Mondanaro A, Melchionna M, Febbraro MD, Sansalone G, Wroe S, Raia P (2020). “The influence of domestication, insularity and sociality on the tempo and mode of brain size evolution in mammals.” Biological Journal of the Linnean Society, 132, 221-231. https://doi.org/10.1093/biolinnean/blaa186.

conv.map

Melchionna M, Profico A, Castiglione S, Serio C, Mondanaro A, Modafferi M, Tamagnini D, Maiorano L, Raia P, Witmer LM, Wroe S, Sansalone G (2021). “A method for mapping morphological convergence on three-dimensional digital models: the case of the mammalian sabre-tooth.” Palaeontology, 64, 573–584. https://doi.org/10.1111/pala.12542.

Corresponding BibTeX entries:

  @Article{,
    title = {A new method for testing evolutionary rate variation and
      shifts in phenotypic evolution.},
    author = {Silvia Castiglione and Gianmarco Tesone and Martina
      Piccolo and Marina Melchionna and Alessandro Mondanaro and
      Carmela Serio and Mirko Di Febbraro and Pasquale Raia},
    journal = {Methods in Ecology and Evolution},
    year = {2018},
    volume = {9},
    pages = {974-983},
    url =
      {https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.12954},
  }
  @Article{,
    title = {Macroevolution of toothed whales exceptional relative
      brain size.},
    author = {Carmela Serio and Silvia Castiglione and Gianmarco Tesone
      and Martina Piccolo and Marina Melchionna and Alessandro
      Mondanaro and Mirko Di Febbraro and Pasquale Raia},
    journal = {Evolutionary Biology},
    year = {2019},
    volume = {46},
    pages = {332-342},
    url =
      {https://link.springer.com/article/10.1007/s11692-019-09485-7},
  }
  @Article{,
    title = {Macroevolutionary trends of brain mass in Primates.},
    author = {Marina Melchionna and Alessandro Mondanaro and Carmela
      Serio and Silvia Castiglione and Mirko Di Febbraro and Lorenzo
      Rook and José Alexandre Diniz-Filho and Giorgio Manzi and Antonio
      Profico and Gabriele Sansalone and Pasquale Raia},
    journal = {Biological Journal of the Linnean Society},
    year = {2020},
    url =
      {https://academic.oup.com/biolinnean/advance-article/doi/10.1093/biolinnean/blz161/5614248},
  }
  @Article{,
    title = {Ancestral State Estimation with Phylogenetic Ridge
      Regression},
    author = {Silvia Castiglione and Carmela Serio and Alessandro
      Mondanaro and Marina Melchionna and Francesco Carotenuto and
      Mirko Di Febbraro and Antonio Profico and Davide Tamagnini and
      Pasquale Raia},
    journal = {Evolutionary Biology},
    year = {2020},
    volume = {47},
    pages = {220-232},
    url =
      {https://link.springer.com/article/10.1007/s11692-020-09505-x},
  }
  @Article{,
    title = {Simultaneous detection of macroevolutionary patterns in
      phenotypic means and rate of change with and within phylogenetic
      trees including extinct species.},
    author = {Silvia Castiglione and Carmela Serio and Alessandro
      Mondanaro and Mirko Di Febbraro and Antponio Profico and Giorgia
      Girardi and Pasquale Raia},
    journal = {PLoS ONE},
    year = {2019},
    volume = {14},
    pages = {e0210101},
    url =
      {https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0210101},
  }
  @Article{,
    title = {A new, fast method to search for morphological convergence
      with shape data.},
    author = {Silvia Castiglione and Carmela Serio and Davide Tamagnini
      and Marina Melchionna and Alessandro Mondanaro and Mirko Di
      Febbraro and Antonio Profico and Paolo Piras and Filippo
      Barattolo and Pasquale Raia},
    journal = {PLoS ONE},
    year = {2019},
    volume = {14},
    pages = {e0226949},
    url = {https://doi.org/10.1371/journal.pone.0226949},
  }
  @Article{,
    title = {The influence of domestication, insularity and sociality
      on the tempo and mode of brain size evolution in mammals.},
    author = {Silvia Castiglione and Carmela Serio and Martina Piccolo
      and Alessandro Mondanaro and Marina Melchionna and Mirko Di
      Febbraro and Gabriele Sansalone and Stephen Wroe and Pasquale
      Raia},
    journal = {Biological Journal of the Linnean Society},
    year = {2020},
    volume = {132},
    pages = {221-231},
    url = {https://doi.org/10.1093/biolinnean/blaa186},
  }
  @Article{,
    title = {A method for mapping morphological convergence on
      three-dimensional digital models: the case of the mammalian
      sabre-tooth},
    author = {Marina Melchionna and Antonio Profico and Silvia
      Castiglione and Carmela Serio and Alessandro Mondanaro and Maria
      Modafferi and Davide Tamagnini and Luigi Maiorano and Pasquale
      Raia and Lawrence M. Witmer and Stephen Wroe and Gabriele
      Sansalone},
    journal = {Palaeontology},
    year = {2021},
    volume = {64},
    pages = {573–584},
    url = {https://doi.org/10.1111/pala.12542},
  }