This is a repository for our paper "Drivers of phylogenetic assemblage structure of the Furnariides, a widespread clade of lowland Neotropical birds" published in The American Naturalist.
The repository includes the R functions to run DAMOCLES model over multiple assemblages. This respository also includes the R scripts for plotting the results.
"DemonDAMOCLES" is a R wrapper function to run DAMOCLES model (r package DAMOCLES; Pigot & Etienne 2015 Ecology Letters 18, 153-163) for multiple local assemblages in parallel.
If you want to replicate our analyses, please download the Furnariides phylogeny and the assemblage data set from the Dryad repository: https://doi.org/10.5061/dryad.h3390h5
Note: Damocles model is very time-consuming.
Pigot, A.L. and R.S. Etienne (2015) A new dynamic null model for phylogenetic community structure. Ecology Letters 18, 153-163.
Pinto-Ledezma, J.N., A.E. Jahn, V.R. Cueto, J.A.F. Diniz-Filho and F. Villalobos (2019) Drivers of phylogenetic assemblage structure of the Furnariides, a widespread clade of lowland Neotropical birds. The American Naturalist, 193(2): E41-E56. https://www.journals.uchicago.edu/doi/abs/10.1086/700696
A correction can be found in: Pinto-Ledezma, J.N., A.E. Jahn, V.R. Cueto, J.A.F. Diniz-Filho and F. Villalobos (2019) Correction. The American Naturalist 193(6): 897. https://www.journals.uchicago.edu/doi/abs/10.1086/703185
Pinto-Ledezma, J.N., A.E. Jahn, V.R. Cueto, J.A.F. Diniz-Filho and F. Villalobos (2018) Drivers of phylogenetic assemblage structure of the Furnariides, a widespread clade of lowland Neotropical birds. The American Naturalist, Dryad Digital Repository, https://datadryad.org/resource/doi:10.5061/dryad.h3390h5