get_trait_stats_over_time: Calculate mean & standard deviation of a numeric trait on a...

In castor: Efficient Phylogenetics on Large Trees

Calculate mean & standard deviation of a numeric trait on a dated tree over time.

Description

Given a rooted and dated phylogenetic tree, and a scalar numeric trait with known value on each node and tip of the tree, calculate the mean and the variance of the trait's states across the tree at discrete time points. For example, if the trait represents "body size", then this function calculates the mean body size of extant clades over time.

Usage

get_trait_stats_over_time(tree,
                          states, 
                          Ntimes            = NULL,
                          times             = NULL,
                          include_quantiles = TRUE,
                          check_input       = TRUE)

Arguments

tree	A rooted tree of class "phylo", where edge lengths represent time intervals (or similar).
states	Numeric vector, specifying the trait's state at each tip and each node of the tree (in the order in which tips & nodes are indexed). May include NA or NaN if values are missing for some tips/nodes.
Ntimes	Integer, number of equidistant time points for which to calculade clade counts. Can also be NULL, in which case times must be provided.
times	Integer vector, listing time points (in ascending order) for which to calculate clade counts. Can also be NULL, in which case Ntimes must be provided.
include_quantiles	Logical, specifying whether to include information on quantiles (e.g., median, CI95, CI50) of the trait over time, in addition to the means and standard deviations. This option increases computation time and memory needs for large trees, so if you only care about means and standard deviations you can set this to FALSE.
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

If tree$edge.length is missing, then every edge in the tree is assumed to be of length 1. The tree may include multi-furcations as well as mono-furcations (i.e. nodes with only one child). The tree need not be ultrametric (e.g. may include extinct tips), although in general this function only makes sense if edge lengths correspond to time (or similar).

Either Ntimes or times must be non-NULL, but not both. states need not include names; if it does, then these are checked to be in the same order as in the tree (if check_input==TRUE).

Value

A list with the following elements:

Ntimes	Integer, indicating the number of returned time points. Equal to the provided Ntimes if applicable.
times	Numeric vector of size Ntimes, listing the considered time points in increasing order. If times was provided as an argument to the function, then this will be the same as provided.
clade_counts	Integer vector of size Ntimes, listing the number of tips or nodes considered at each time point.
means	Numeric vector of size Ntimes, listing the arithmetic mean of trait states at each time point.
stds	Numeric vector of size Ntimes, listing the standard deviation of trait states at each time point.
medians	Numeric vector of size Ntimes, listing the median trait state at each time point. Only returned if include_uantiles=TRUE.
CI50lower	Numeric vector of size Ntimes, listing the lower end of the equal-tailed 50% range of trait states (i.e., the 25% percentile) at each time point. Only returned if include_uantiles=TRUE.
CI50upper	Numeric vector of size Ntimes, listing the upper end of the equal-tailed 50% range of trait states (i.e., the 75% percentile) at each time point. Only returned if include_uantiles=TRUE.
CI95lower	Numeric vector of size Ntimes, listing the lower end of the equal-tailed 95% range of trait states (i.e., the 2.5% percentile) at each time point. Only returned if include_uantiles=TRUE.
CI95upper	Numeric vector of size Ntimes, listing the upper end of the equal-tailed 95% range of trait states (i.e., the 97.5% percentile) at each time point. Only returned if include_uantiles=TRUE.

Author(s)

Stilianos Louca

Examples

# generate a random tree
tree = generate_random_tree(list(birth_rate_intercept=1), max_tips=1000)$tree

# simulate a numeric trait under Brownian-motion
trait = simulate_bm_model(tree, diffusivity=1)
states = c(trait$tip_states,trait$node_states)

# calculate trait stats over time
results = get_trait_stats_over_time(tree, states, Ntimes=100)

# plot trait stats over time (mean +/- std)
M = results$means
S = results$stds
matplot(x=results$times, 
        y=matrix(c(M-S,M+S),ncol=2,byrow=FALSE),
        main = "Simulated BM trait over time",
        lty = 1, col="black",
        type="l", xlab="time", ylab="mean +/- std")

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