Claddis (version 0.3.4)

AncStateEstMatrix: Ancestral Character State Estimation

Description

Given a tree and a cladistic matrix uses likelihood to estimate the ancestral states for every character.

Usage

AncStateEstMatrix(CladisticMatrix, Tree, EstimateAllNodes = FALSE,
  EstimateTipValues = FALSE, InapplicablesAsMissing = FALSE,
  PolymorphismBehaviour = "equalp", UncertaintyBehaviour = "equalp",
  Threshold = 0.01)

Arguments

CladisticMatrix

A character-taxon matrix in the format imported by ReadMorphNexus.

Tree

A tree (phylo object) with branch lengths that represents the relationships of the taxa in CladisticMatrix.

EstimateAllNodes

Logical that allows the user to make estimates for all ancestral values. The default (FALSE) will only make estimates for nodes that link coded terminals (recommended).

EstimateTipValues

Logical that allows the user to make estimates for tip values. The default (FALSE) will only makes estimates for internal nodes (recommended).

InapplicablesAsMissing

Logical that decides whether or not to treat inapplicables as missing (TRUE) or not (FALSE, the default and recommended option).

PolymorphismBehaviour

One of either "equalp" or "treatasmissing".

UncertaintyBehaviour

One of either "equalp" or "treatasmissing".

Threshold

The threshold value to use when collapsing marginal likelihoods to discrete state(s).

Value

anc.lik.matrix

A matrix of nodes (hypothetical ancestors; rows) against characters (columns) listing the reconstructed ancestral states.

Details

Uses either the rerootingMethod (Yang et al. 1995) as implemented in the phytools package (discrete characters) or the ace function in the ape package (continuous characters) to make ancestral state estimates. For discrete characters these are collapsed to the most likely state (or states, given equal likelihoods or likelihood within a defined threshold value). In the latter case the resulting states are represented as an uncertainty (i.e., states separated by a slash, e.g., 0/1. This is the method used by Brusatte et al. (2014).

References

Brusatte, S. L., Lloyd, G. T., Wang, S. C. and Norell, M. A., 2014. Gradual assembly of avian body plan culminated in rapid rates of evolution across dinosaur-bird transition. Current Biology, 24, 2386-2392.

Yang, Z., Kumar, S. and Nei, M., 1995. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics, 141, 1641-1650.

Examples

# NOT RUN {
# Set random seed:
set.seed(4)

# Generate a random tree for the Day data set:
tree <- rtree(n = nrow(Day2016$Matrix_1$Matrix))

# Update taxon names to match those in the data matrix:
tree$tip.label <- rownames(Day2016$Matrix_1$Matrix)

# Set root time by making youngest taxon extant:
tree$root.time <- max(diag(vcv(tree)))

# Use Day matrix as cladistic matrix:
CladisticMatrix <- Day2016

# Prune most characters out to make example run fast:
CladisticMatrix <- MatrixPruner(CladisticMatrix,
  characters2prune = c(2:3, 5:37))

# Estimate ancestral states:
AncStateEstMatrix(CladisticMatrix = CladisticMatrix,
  Tree = tree)

# }