Author: Barnabas H. Daru
Date: 2022-11-16

# Fast Evolutionary Distinctiveness

#### Barnabas H. Daru

#### November 16, 2022

## Introduction

Evolutionary distinctiveness is a metric that quantifies how isolated a species is on a phylogenetic tree – some species have few or no close living relatives.

The standard method for calculating evolutionary distinctiveness is either by using the `R` packages `picante` or `caper`. For very large trees, such calculation is a memory-intensive operation and a bottle-neck for these algorithms.

Because of these challenges, we developed a new method in our `phyloregion` package that speeds up the process significantly to produce results in seconds! See how:

Let’s try computing evolutionary distinctiveness for a tree with 5,000 species:

    library(ape)
    library(ggplot2)
    # packages we benchmark
    library(phyloregion)
    library(picante)
    library(caper)

    tree <- ape::rcoal(5000)

    ed_picante <- function(x) picante::evol.distinct(x, type="fair.proportion")
    ed_caper <- function(x) caper::ed.calc(x)
    ed_phyloregion <- function(x) phyloregion::evol_distinct(x, type="fair.proportion")

    res <- bench::mark(picante=ed_picante(tree),
              caper=ed_caper(tree),
              phyloregion=ed_phyloregion(tree), check=FALSE)
    summary(res)

    ## # A tibble: 3 × 6
    ##   expression       min   median `itr/sec` mem_alloc `gc/sec`
    ##   <bch:expr>  <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
    ## 1 picante        4.02m    4.02m   0.00415        NA    18.9
    ## 2 caper          9.17s    9.17s   0.109          NA     5.45
    ## 3 phyloregion   65.3ms  70.56ms  13.9            NA     1.98

    autoplot(res)

Here, `phyloregion` is several orders of magnitude faster and efficient in memory allocation than the other packages.

The function in `phyloreegion` is called `evol_distinct` and it is used as follows:

    evol_distinct(tree, type = c("equal.splits", "fair.proportion"), ...)

If you find this vignette tutorial useful, please cite in publications as:

Daru, B.H., Karunarathne, P. & Schliep, K. (2020) phyloregion: R package for biogeographic regionalization and macroecology. Methods in Ecology and Evolution 11: 1483-1491. doi: 10.1111/2041-210X.13478.