discrete_trait_depth: Calculate phylogenetic depth of a discrete trait.

In castor: Efficient Phylogenetics on Large Trees

Calculate phylogenetic depth of a discrete trait.

Description

Given a rooted phylogenetic tree and the state of a discrete trait at each tip, calculate the mean phylogenetic depth at which the trait is conserved across clades, using a modification of the consenTRAIT metric introduced by Martiny et al (2013). This is the mean depth of clades that are "maximally uniform" in the trait (see below for details).

Usage

discrete_trait_depth(tree, 
                     tip_states, 
                     min_fraction         = 0.9, 
                     count_singletons     = TRUE,
                     singleton_resolution = 0,
                     weighted             = FALSE, 
                     Npermutations        = 0)

Arguments

tree	A rooted tree of class "phylo". The root is assumed to be the unique node with no incoming edge.
tip_states	A vector of size Ntips specifying the state at each tip. Note that tip_states[i] (where i is an integer index) must correspond to the i-th tip in the tree. This vector may be of any base data type, although character or integer are the most typical types.
min_fraction	Minimum fraction of tips in a clade that must have the dominant state, for the clade to be considered "uniform" in the trait.
count_singletons	Logical, specifying whether to consider singleton clades in the statistics (e.g., tips not part of a larger uniform clade). The phylogenetic depth of singletons is taken to be half the length of their incoming edge, as proposed by Martiny et al (2013). If FALSE, singletons are ignored. If you suspect a high risk of false positives in the detection of a trait, it may be worth setting count_singletons to FALSE to avoid skewing the distribution of conservation depths towards shallower depths due to false positives.
singleton_resolution	Numeric, specifying the phylogenetic resolution at which to resolve singletons. A clade will be considered a singleton if the distance of the clade's root to all descending tips is below this threshold.
weighted	Whether to weight uniform clades by their number of tips in the dominant state. If FALSE, each uniform clades is weighted equally.
Npermutations	Number of random permutations for estimating the statistical significance of the mean trait depth. If zero (default), the statistical significance is not calculated.

Details

The depth of a clade is defined as the average distance of its tips to the clade's root. The "dominant" state of a clade is defined as the most frequent state among all of the clade's tips. A clade is considered "uniform" in the trait if the frequency of its dominant state is equal to or greater than min_fraction. The clade is "maximally uniform" if it is uniform and not descending from another uniform clade. The mean depth of the trait is defined as the average phylogenetic depth of all considered maximal uniform clades (whether a maximally uniform clade is considered in this statistic depends on count_singletons and singleton_resolution). A greater mean depth means that the trait tends to be conserved in deeper-rooting clades.

This function implements a modification of the "consenTRAIT" metric proposed by Martiny et al. (2013) for measuring the mean phylogenetic depth at which a binary trait is conserved across clades. Note that the original consenTRAIT metric by Martiny et al. (2013) does not treat the two states of a binary trait ("presence" and "absence") equally, whereas the function discrete_trait_depth does. If you want the original consenTRAIT metric for a binary trait, see the function consentrait_depth.

The statistical significance of the calculated mean depth, i.e. the probability of encountering such a mean dept or higher by chance, is estimated based on a null model in which each tip is re-assigned a state by randomly reshuffling the original tip_states. A low P value indicates that the trait exhibits a phylogenetic signal, whereas a high P value means that there is insufficient evidence in the data to suggest a phylogenetic signal (i.e., the trait's phylogenetic conservatism is indistinguishable from the null model of zero conservatism).

The tree may include multi-furcations as well as mono-furcations (i.e. nodes with only one child). If tree$edge.length is missing, then every edge is assumed to have length 1.

Value

A list with the following elements:

unique_states	Vector of the same type as tip_states and of length Nstates, listing the unique possible states of the trait.
mean_depth	Numeric, specifying the mean phylogenetic depth of the trait, i.e., the mean depth of considered maximally uniform clades.
var_depth	Numeric, specifying the variance of phylogenetic depths of considered maximally uniform clades.
min_depth	Numeric, specifying the minimum phylogenetic depth of considered maximally uniform clades.
max_depth	Numeric, specifying the maximum phylogenetic depth of considered maximally uniform clades.
Nmax_uniform	Number of considered maximal uniform clades.
mean_depth_per_state	Numeric vector of size Nstates. Mean depth of considered maximally uniform clades, separately for each state and in the same order as unique_states. Hence, mean_depth_per_state[s] lists the mean depth of considered maximally uniform clades whose dominant state is unique_states[s].
var_depth_per_state	Numeric vector of size Nstates. Variance of depths of considered maximally uniform clades, separately for each state and in the same order as unique_states
min_depth_per_state	Numeric vector of size Nstates. Minimum phylogenetic depth of considered maximally uniform clades, separately for each state and in the same order as unique_states
max_depth_per_state	Numeric vector of size Nstates. Maximum phylogenetic depth of considered maximally uniform clades, separately for each state and in the same order as unique_states
Nmax_uniform_per_state	Integer vector of size Nstates. Number of considered maximally uniform clades, seperately for each state and in the same order as unique_states
P	Statistical significance (P-value) of mean_depth, under a null model of random tip states (see details above). This is the probability that, under the null model, the mean_depth would be at least as high as observed in the data.
mean_random_depth	Mean random mean_depth, under the null model of random tip states (see details above).

Author(s)

Stilianos Louca

References

A. C. Martiny, K. Treseder and G. Pusch (2013). Phylogenetic trait conservatism of functional traits in microorganisms. ISME Journal. 7:830-838.

See Also

get_trait_acf, consentrait_depth

Examples

## Not run: 
# generate a random tree
tree = generate_random_tree(list(birth_rate_intercept=1),max_tips=1000)$tree

# simulate discrete trait evolution on the tree
# consider a trait with 3 discrete states
Q = get_random_mk_transition_matrix(Nstates=3, rate_model="ARD", max_rate=0.1)
tip_states = simulate_mk_model(tree, Q)$tip_states

# calculate phylogenetic conservatism of trait
results = discrete_trait_depth(tree, tip_states, count_singletons=FALSE, weighted=TRUE)
cat(sprintf("Mean depth = %g, std = %g\n",results$mean_depth,sqrt(results$var_depth)))

## End(Not run)

castor documentation built on June 29, 2024, 9:08 a.m.