To cite RRphylo implementations and auxilliary functions in publications use:

RRphylo package, search.shift, and auxilliary functions

Silvia Castiglione, Gianmarco Tesone, Martina Piccolo, Marina Melchionna, Alessandro Mondanaro, Carmela Serio, Mirko Di Febbraro, Pasquale Raia (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

Carmela Serio, Silvia Castiglione, Gianmarco Tesone, Martina Piccolo, Marina Melchionna, Alessandro Mondanaro, Mirko Di Febbraro, Pasquale Raia (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.

Marina Melchionna, Alessandro Mondanaro, Carmela Serio, Silvia Castiglione, Mirko Di Febbraro, Lorenzo Rook, José Alexandre Diniz-Filho, Giorgio Manzi, Antonio Profico, Gabriele Sansalone, Pasquale Raia (2020). “Macroevolutionary trends of brain mass in Primates.” Biological Journal of the Linnean Society, 129, 14-25. doi:10.1093/biolinnean/blz161.

Ancestral state integration in RRphylo (RRphylo-noder)

Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Francesco Carotenuto, Mirko Di Febbraro, Antonio Profico, Davide Tamagnini, Pasquale Raia (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

Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Mirko Di Febbraro, Antponio Profico, Giorgia Girardi, Pasquale Raia (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

Silvia Castiglione, Carmela Serio, Davide Tamagnini, Marina Melchionna, Alessandro Mondanaro, Mirko Di Febbraro, Antonio Profico, Paolo Piras, Filippo Barattolo, Pasquale Raia (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

Silvia Castiglione, Carmela Serio, Martina Piccolo, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Gabriele Sansalone, Stephen Wroe, Pasquale Raia (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

Marina Melchionna, Antonio Profico, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Maria Modafferi, Davide Tamagnini, Luigi Maiorano, Pasquale Raia, Lawrence M. Witmer, Stephen Wroe, Gabriele Sansalone (2021). “A method for mapping morphological convergence on three-dimensional digital models: the case of the mammalian sabre-tooth.” Palaeontology, 64, 573–584. https://onlinelibrary.wiley.com/doi/10.1111/pala.12542.

rate.map

Silvia Castiglione, Marina Melchionna, Antonio Profico, Gabriele Sansalone, Maria Modafferi, Alessandro Mondanaro, Stephen Wroe, Paolo Piras, Pasquale Raia (2021). “Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models.” Palaeontology, 65, e12582. https://onlinelibrary.wiley.com/doi/10.1111/pala.12582.

tree.merger

Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Pasquale Raia (2022). “Fast Production of Large, Time-Calibrated Informal Supertrees with tree.merger.” Palaeontology, 65, e12588. https://onlinelibrary.wiley.com/doi/10.1111/pala.12588.

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},
    volume = {129},
    pages = {14-25},
    doi = {10.1093/biolinnean/blz161},
  }

  @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://onlinelibrary.wiley.com/doi/10.1111/pala.12542},
  }

  @Article{,
    title = {Human face-off: a new method for mapping evolutionary
      rates on three-dimensional digital models},
    author = {{Silvia Castiglione} and {Marina Melchionna} and {Antonio
      Profico} and {Gabriele Sansalone} and {Maria Modafferi} and
      {Alessandro Mondanaro} and {Stephen Wroe} and {Paolo Piras} and
      {Pasquale Raia}},
    journal = {Palaeontology},
    year = {2021},
    volume = {65},
    pages = {e12582},
    url = {https://onlinelibrary.wiley.com/doi/10.1111/pala.12582},
  }

  @Article{,
    title = {Fast Production of Large, Time-Calibrated Informal
      Supertrees with tree.merger},
    author = {{Silvia Castiglione} and {Carmela Serio} and {Alessandro
      Mondanaro} and {Marina Melchionna} and {Pasquale Raia}},
    journal = {Palaeontology},
    year = {2022},
    volume = {65},
    pages = {e12588},
    url = {https://onlinelibrary.wiley.com/doi/10.1111/pala.12588},
  }