hsp_subtree_averaging: Hidden state prediction via subtree averaging.

In castor: Efficient Phylogenetics on Large Trees

Hidden state prediction via subtree averaging.

Description

Reconstruct ancestral states of a continuous (numeric) trait for nodes and predict unknown (hidden) states for tips on a tree using subtree averaging.

Usage

hsp_subtree_averaging(tree, tip_states, check_input=TRUE)

Arguments

tree	A rooted tree of class "phylo". The root is assumed to be the unique node with no incoming edge.
tip_states	A numeric vector of size Ntips, specifying the state of each tip in the tree. tip_states can include NA to indicate an unknown tip state that is to be predicted.
check_input	Logical, specifying whether to perform some basic checks on the validity of the input data. If you are certain that your input data are valid, you can set this to FALSE to reduce computation.

Details

Any NA entries in tip_states are interpreted as unknown (hidden) states to be estimated. For each node the reconstructed state is set to the arithmetic average state of all tips with known state and descending from that node. For each tip with hidden state and each node whose descending tips all have hidden states, the state is set to the state of the closest ancestral node with known or reconstructed state, while traversing from root to tips (Zaneveld and Thurber 2014). Note that reconstructed node states are only local estimates, i.e. for each node the estimate is only based on the tip states in the subtree descending from that node.

Tips must be represented in tip_states in the same order as in tree$tip.label. The vector tip_states need not include item names; if it does, however, they are checked for consistency (if check_input==TRUE). This function has asymptotic time complexity O(Nedges).

This function is meant for reconstructing ancestral states in all nodes of a tree as well as predicting the states of tips with an a priory unknown state. If the state of all tips is known and only ancestral state reconstruction is needed, consider using the function asr_subtree_averaging for improved efficiency.

Value

A list with the following elements:

success	Logical, indicating whether HSP was successful.
states	A numeric vector of size Ntips+Nnodes, listing the reconstructed state of each tip and node. The entries in this vector will be in the order in which tips and nodes are indexed in tree$edge.

Author(s)

Stilianos Louca

References

J. R. Zaneveld and R. L. V. Thurber (2014). Hidden state prediction: A modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses. Frontiers in Microbiology. 5:431.

See Also

asr_subtree_averaging, hsp_squared_change_parsimony

Examples

# generate random tree
Ntips = 100
tree = generate_random_tree(list(birth_rate_intercept=1),max_tips=Ntips)$tree

# simulate a continuous trait
tip_states = simulate_ou_model(tree,
                               stationary_mean=0,
                               stationary_std=1,
                               decay_rate=0.001)$tip_states

# print tip states
print(as.vector(tip_states))

# set half of the tips to unknown state
tip_states[sample.int(Ntips,size=as.integer(Ntips/2),replace=FALSE)] = NA

# reconstruct all tip states via subtree averaging
estimated_states = hsp_subtree_averaging(tree, tip_states)$states

# print estimated tip states
print(estimated_states[1:Ntips])

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