Description Details Author(s) References Examples

The package implements Borregaard et al. (2014) method for identifying nodes in a phylogeny associated with divergent distributions. The main algorithm goes through each node in the phylogeny and relates node overlap to a null model. The package also provides functions for preparing the data sets, for exploratory plots and further analysis.

Package: | nodiv |

Type: | Package |

Version: | 1.4.0 |

Date: | 2020-05-26 |

License: | MIT |

The workflow starts by creating a `nodiv_data`

data object, which makes sure that the phylogeny, the species distributions and the spatial coordinates of sites are matched correctly. The function takes a number of data types. There are several functions for exploratory data analysis, including `plot`

, `summary`

, `richness`

, `Node_occupancy`

, `Node_size`

etc. The core of the package are the functions `Nodesig`

, which compares the distributions of the two clades descending from a node, and `Node_analysis`

, which applies this function to all nodes in the phylogeny and summarizes the results as a `nodiv_result`

object. There is a set of functions for interpretation of the results, including `plot`

, `plotSOS`

, and `summary`

. The package also provides basic functions for plotting and manipulating data sets that combine spatial distributions with phylogenies, e.g. `subsample`

, `plot_grid`

and `plot_points`

.
Note that the package may still be unstable - if you experience problems, try cloning the github repository instead: `library(devtools); install_github("mkborregaard/nodiv")`

, or feel free to contact the maintainer.

Michael Krabbe Borregaard

Maintainer: Michael Krabbe Borregaard <mkborregaard@sund.ku.dk>

Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. <DOI:10.1111/2041-210X.12283>

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