nodiv: Compares the Distribution of Sister Clades Through a Phylogeny

An implementation of the nodiv algorithm, see 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>. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.

Author
Michael Krabbe Borregaard
Date of publication
2016-02-10 09:11:19
Maintainer
Michael Krabbe Borregaard <mkborregaard@snm.ku.dk>
License
GPL-3
Version
1.1.4

View on CRAN

Man pages

add_shape
Add a shapefile to a 'nodiv' data object
add_sitestat
Site statistics of 'nodiv' data objects
add_species_stat
Species statistics of 'nodiv' data objects
basal_node
Identify nodes in a phylogeny
coquettes
Distribution of coquette hummingbirds in Northern South...
distrib_data
Data objects for node-based analysis
gridData
Apply a grid (2D bins) to nodiv objects of type 'points'
Node_analysis
Calculate GND and SOS scores for a phylogeny and community...
Nodesig
Compare the distributions of a pair of sister clades
Node_size
Attributes of individual clades
nodiv-package
nodiv - Node-based analysis of species distributions
Nspecies
Basic attributes of 'distrib_data' objects
occurrences
Access functions to the community matrix of 'distrib_data'...
phyplot
Plot Phylogenies
plot_nodes_phylo
Plot a phylogeny with colored node labels
plot_points
Plot a variable on spatial points or a spatial grid using a...
plot_richness
Plot a richness map for an object of type distrib_data,...
plotSOS
Gives the SOS values for a given node.
read.tree
Read Tree File in Parenthetic Format
subsample
Subsampling data objects to certain species or sites
two_color_map
Plot the relative amounts of two variables using a...
update_object
Update 'distrib_data' objects to the 'nodiv' version >= 1.1...

Files in this package

nodiv
nodiv/inst
nodiv/inst/CITATION
nodiv/tests
nodiv/tests/testthat.R
nodiv/tests/testthat
nodiv/tests/testthat/test_access.R
nodiv/tests/testthat/test_basic_functions.R
nodiv/NAMESPACE
nodiv/data
nodiv/data/coquettes.rda
nodiv/R
nodiv/R/Node_based_analysis.R
nodiv/R/Add_to_data_object.R
nodiv/R/colors.R
nodiv/R/General_figure_functions.R
nodiv/R/Methods_for_result_objects.R
nodiv/R/Node_analysis_function.R
nodiv/R/Methods_for_data_objects.R
nodiv/R/Prepare_result_object.R
nodiv/R/two_color_map.R
nodiv/R/Nodesig_function.R
nodiv/R/Prepare_data.R
nodiv/MD5
nodiv/DESCRIPTION
nodiv/man
nodiv/man/add_species_stat.Rd
nodiv/man/distrib_data.Rd
nodiv/man/Nodesig.Rd
nodiv/man/plot_nodes_phylo.Rd
nodiv/man/coquettes.Rd
nodiv/man/add_sitestat.Rd
nodiv/man/plot_richness.Rd
nodiv/man/basal_node.Rd
nodiv/man/read.tree.Rd
nodiv/man/two_color_map.Rd
nodiv/man/plotSOS.Rd
nodiv/man/Nspecies.Rd
nodiv/man/gridData.Rd
nodiv/man/subsample.Rd
nodiv/man/nodiv-package.Rd
nodiv/man/update_object.Rd
nodiv/man/Node_size.Rd
nodiv/man/phyplot.Rd
nodiv/man/occurrences.Rd
nodiv/man/Node_analysis.Rd
nodiv/man/plot_points.Rd
nodiv/man/add_shape.Rd