Grouse, Kenya
© Nick Crouch
RDH: Range data helper. A package designed to aid in the analysis of spatial data. The package is available via GitHub
I have also contributed code snippets to paleotree and rwty
Individual functions
Oct 24th 2014
phylo.diversity : Will calculate diversity of groups through time, given a phylogeny and information on which groups the species belong to.
Dec 9th 2014
add.tip.icons : Plot discrete species characters onto a phylogeny.
Jan 15th 2015
add_HPD_info : Add posterior age distribution information to specified nodes on a phylogeny Updated Nov 2nd 2015 .
Feb 24th 2015
base.line.values : Calculate base line origination and extinction values, following Foote (2005).
Sept 8th 2015
unique_sister_spp: Calculates the number of unique sister species for a range of species across a set of phylogenies. This function is currently being implemented in the R package rwty.
Oct 8th 2015
color.terminal.branches: Color only the terminal branches in a phylogeny by corresponding species trait values Updated Jan 26th 2017 .
Feb 16th 2016
calculate.ellipse.area: Calculate the amount of morphological space occupied by taxa.
Sept 20th 2016
migration.distance: Calculate the migration distance for a specified species.
Aug 16th 2017
mirror.barplot: Make a mirrored barplot for comparing positive and negative changes in a variable.
Aug 18th 2017
make.node.age.df: Extract node age information from an annotated phylogeny.
Jun 14th 2018
branch.length.diff: Visualize how terminal branch lengths differ between two sets of phylogenies.
Nov 21st 2018
fixLineBreaks: Remove line breaks from alignment files to allow them to be read into R.
Dec 5th 2018
characters.supporting.clade: Find those characters in an alignment that support the relationship between specified taxa.
Jan 15th 2019
make.inp.format: Convert occurence data from the Paleobiology Database into .inp format for downstream analyses.
Apr 16th 2019
phylo.ternary.plot: Display the results of three branch-length transformations on a single phylogeny.
May 6th 2019
boxplot.by.node : Plot a boxplot next to a phylogeny in order of nodes for which the data is from.
Aug 22nd 2019
time.to.rateshift.node : Quantify the amount of time estimated shifts in diversification dynamics occur before target nodes.
Nov 24th 2020
plot.shared.nodes : Compare topologies across a set of phylogenies, coloring nodes by whether it is concordant or different .