README.md

In alrobles/geotax: Tools for exploring taxonomic distance over the geographical space

geotax

This packages aims to model the probability that two host share a pathogen given a phylogenetic (or taxonomic) distance. Please link to the original paper

Installation

You can install the development version of geotax from GitHub with:

# install.packages("devtools")
devtools::install_github("alrobles/geotax")

Examples

geotax comes with basic tools. For example compute a taxonomic tree from a table with taxonomic ranks. In this example we load a taxonomic tree of species that has been record with bark beetles. We use the table provide in the paper.

We can also plot this tree and explore the distance matrix with the help of ape package

library(geotax)
library(dplyr) ## this is for clean the data if need it
#> Warning: package 'dplyr' was built under R version 4.1.3
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
data("tax_table")
clean_tree <- distinct(tax_table)

# clean the data
taxonomic_tree <- geotax::get_taxonomical_tree(clean_tree, power = 1)
plot(taxonomic_tree, type = "radial", show.tip.label = FALSE)

ape::cophenetic.phylo(taxonomic_tree)[1:5, 1:5]
#>                       Lysiloma latisiliquum Ormosia hosiei Cercis canadensis
#> Lysiloma latisiliquum             0.0000000      0.2857143         0.2857143
#> Ormosia hosiei                    0.2857143      0.0000000         0.2857143
#> Cercis canadensis                 0.2857143      0.2857143         0.0000000
#> Dialium guianense                 0.2857143      0.2857143         0.2857143
#> Vachellia pennatula               0.2857143      0.2857143         0.2857143
#>                       Dialium guianense Vachellia pennatula
#> Lysiloma latisiliquum         0.2857143           0.2857143
#> Ormosia hosiei                0.2857143           0.2857143
#> Cercis canadensis             0.2857143           0.2857143
#> Dialium guianense             0.0000000           0.2857143
#> Vachellia pennatula           0.2857143           0.0000000

alrobles/geotax documentation built on July 27, 2023, 4:37 a.m.