treestats
| Branch | CodeCov |
|---|---|
| master |  |
| develop |  |
Description
R package that combines functions to calculate summary statistics on phylogenies. The following summary statistics are included:
- Aldous Beta
- Sackin index
- Colless index
- Equal Weights Colless Index
- Blum index
- Crown age
- Tree height
- Pigot's Rho
- Mean branch length
- Number of lineages
- Laplacian spectrum
- nLTT
- Gamma
- Phylogenetic Diversity
- avgLadder
- ILnumber
- pitchforks
- stairs
- stairs2
- Rogers J
- Average Leaf Depth
- Variance Leaf Depth
- I balance index
- Laplacian spectrum properties
- Mean Nearest Taxon Distance
- Mean Pairwise Distance
- Variance Pairwise Distance
- Intensive Quadratic Entropy J
- Phylogenetic Species Variability
- Total Cophenetic index
- B1
- B2
- Max Width
- Max Depth
- Max Del Width
Rcpp
For all of these statistics, the package provides Rcpp versions that are much, much faster than their R sister functions. Furthermore, some additional functions have been improved as well:
- ape::branching.times
- DDD::phylo2L
- DDD::L2phylo
C++ Library
For the Rcpp improved summary statistics (excluding the RPANDA and DDD functions, as these are only partially captured in Rcpp), tree independent C++ code is provided in the inst/include folder. These can be independently linked by adding the treestats package in the DESCRIPTION in both the LinkingTo and Depends fields. Then, in your package, you can also calculate these functions.
Please note that for all functions, there are two versions available:
- based on input of a phylo object, which is typically one 2-column matrix containing all edges, and a vector containing the edge lengths (depending on which information is required to calculate the statistic).
- based on input of an Ltable, which is a 4-column matrix containing information on each species, being 1) birth time, 2) parent species, 3) species label and 4) death time (or -1 if extant).
Ltable input can be useful when summary statistics are required for more complicated simulation models.