secsse (version 3.0.2)

plot_state_exact: Plot the local probability along a tree

Description

Plot the local probability along the tree, including the branches

Usage

plot_state_exact(
  parameters,
  phy,
  traits,
  num_concealed_states,
  sampling_fraction,
  cond = "proper_cond",
  root_state_weight = "proper_weights",
  is_complete_tree = FALSE,
  method = "odeint::bulirsch_stoer",
  atol = 1e-16,
  rtol = 1e-16,
  num_steps = 100,
  prob_func = NULL,
  verbose = FALSE
)

Value

ggplot2 object

Arguments

parameters

list where first vector represents lambdas, the second mus and the third transition rates.

phy

phylogenetic tree of class phylo, rooted and with branch lengths.

traits

vector with trait states for each tip in the phylogeny. The order of the states must be the same as the tree tips. For help, see vignette("starting_secsse", package = "secsse").

num_concealed_states

number of concealed states, generally equivalent to the number of examined states in the dataset.

sampling_fraction

vector that states the sampling proportion per trait state. It must have as many elements as there are trait states.

cond

condition on the existence of a node root: "maddison_cond", "proper_cond" (default). For details, see vignette.

root_state_weight

the method to weigh the states: "maddison_weights", "proper_weights" (default) or "equal_weights". It can also be specified for the root state: the vector c(1, 0, 0) indicates state 1 was the root state.

is_complete_tree

logical specifying whether or not a tree with all its extinct species is provided. If set to TRUE, it also assumes that all all extinct lineages are present on the tree. Defaults to FALSE.

method

integration method used, available are: "odeint::runge_kutta_cash_karp54", "odeint::runge_kutta_fehlberg78", "odeint::runge_kutta_dopri5", "odeint::bulirsch_stoer" and "odeint::runge_kutta4". Default method is: "odeint::bulirsch_stoer".

atol

A numeric specifying the absolute tolerance of integration.

rtol

A numeric specifying the relative tolerance of integration.

num_steps

number of substeps to show intermediate likelihoods along a branch.

prob_func

a function to calculate the probability of interest, see description.

verbose

sets verbose output; default is TRUE when optimmethod is "simplex". If optimmethod is set to "simplex", then even if set to FALSE, optimizer output will be shown.

Details

This function will evaluate the log likelihood locally along all branches and plot the result. When num_steps is left to NULL, all likelihood evaluations during integration are used for plotting. This may work for not too large trees, but may become very memory heavy for larger trees. Instead, the user can indicate a number of steps, which causes the probabilities to be evaluated at a distinct amount of steps along each branch (and the probabilities to be properly integrated in between these steps). This provides an approximation, but generally results look very similar to using the full evaluation. The function used for prob_func will be highly dependent on your system. for instance, for a 3 observed, 2 hidden states model, the probability of state A is prob[1] + prob[2] + prob[3], normalized by the row sum. prob_func will be applied to each row of the 'states' matrix (you can thus test your function on the states matrix returned when 'see_ancestral_states = TRUE'). Please note that the first N columns of the states matrix are the extinction rates, and the (N+1):2N columns belong to the speciation rates, where N = num_obs_states * num_concealed_states. A typical prob_func function will look like:

my_prob_func <- function(x) {
  return(sum(x[5:8]) / sum(x))
}

Examples

set.seed(5)
phy <- ape::rphylo(n = 4, birth = 1, death = 0)
traits <- c(0, 1, 1, 0)
params <- secsse::id_paramPos(c(0, 1), 2)
params[[1]][] <- c(0.2, 0.2, 0.1, 0.1)
params[[2]][] <- 0.0
params[[3]][, ] <- 0.1
diag(params[[3]]) <- NA
#  Thus, we have for both, rates
# 0A, 1A, 0B and 1B. If we are interested in the posterior probability of
# trait 0,we have to provide a helper function that sums the probabilities of
# 0A and 0B, e.g.:
helper_function <- function(x) {
  return(sum(x[c(5, 7)]) / sum(x)) # normalized by total sum, just in case.
}

out_plot <- plot_state_exact(parameters = params,
                             phy = phy,
                             traits = traits,
                             num_concealed_states = 2,
                             sampling_fraction = c(1, 1),
                             num_steps = 10,
                             prob_func = helper_function)