Robust, universal and interpretable tree indices.

Preprint: https://doi.org/10.1101/2023.07.17.549219

The file (or tree) must be in one of the following forms: either a file containing a single tree in Newick or nexus format, or the tree, as a string in Newick format or as a phylo object.

Node abundances must be inputted as a dataframe with two columns. The first column must contain the node labels as given by the inputted tree, the second column must contain the corresponding node abundances. If node abundances are omitted, internal nodes will be assigned size zero and the leaves will be assigned to be equally abundant.

If the given tree does not have branch lengths then they will be assigned to be equal with a length of 1.

To calculate all indices call all_indices(). To calculate either all node mean indices or a single one, call node(). To calculate all longitudinal mean indices, or all star mean indices, or a single of either, call long_star(). The default for the latter two fuctions is to calculate all indices, to calculate one the desired index must be specified.

Examples:

tree <- ape::read.tree(text='(a:1,(b:0.5,c:0.5)e:0.5)d:0;')
na_dataframe <- data.frame("Names" = c("e", "d", "b", "c", "a"), "Values" = c(0, 0, 1/3, 1/3, 1/3))

# Calculate all indices
all_indices(tree, na_dataframe)

# Calculate all node mean indices
node(tree, na_dataframe)

# Calculate all longitudinal mean indices
long_star(tree, na_dataframe, mean_type = "longitudinal")

# Calculate all star mean indices
long_star(tree, na_dataframe, mean_type = "star")

# Calculate single node mean index
node(tree, na_dataframe, index_letter = "D", q = 1, individual = TRUE)

# Calculate single star mean index
long_star(tree, na_dataframe, mean_type = "star", index_letter = "D",
          q = 1, individual = TRUE)