This is what I tried. The problems are described in the comments. Thank you in advance <3
Install necessary packages
install.packages("rotl")
install.packages("ape")
Load required libraries
library(rotl)
library(ape)
Define the list of species
species_list <- c("Panthera leo persica", "Ara glaucogularis", "Helogale parvula”, ”Rangifer tarandus fennicus", "Cebuella pygmaea", "Macropus rufogriseus", "Elaphe taeniura friesei", "Tayassu pecari")
Get OTT ids for the species from the OTL (Tree of life) database
ott_ids <- tnrs_match_names(species_list)$ott_id
print(ott_ids)
Fetch the phylogenetic tree from Open Tree of Life
tree <- tol_induced_subtree(ott_ids = ott_ids)
*## In Console it gives a warning message on singleton nodes
print(tree$tree)
*## In Console: NULL
These would be the next steps that we would do if we wouldn't have gotten stuck
Convert the tree to an 'ape' format
phylo_tree <- ape::read.tree(text=tree$tree)
*## In Console it gives a warning message: In ape::read.tree(text = tree$tree) : empty character string
Calculate distances from humans
distances_from_humans <- cophenetic(phylo_tree)["Homo_sapiens", species_list]
Print the computed distances
print(distances_from_humans)