build_historical_association_matrix: Reconstruct historical association matrix
In treeducken: Nested Phylogenetic Tree Simulator

Description Usage Arguments Details Value Examples

View source: R/build_historical_assoc_mat.R

Reconstruct historical association matrix

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build_historical_association_matrix(t, tr_pair_obj)

get_assoc(t, tr_pair_obj)

`t`	The time of interest
`tr_pair_obj`	The tree pair object from 'sim_cophyBD'

Given a time and a tree pair object produced by the 'sim_cophyBD' object will produce the association matrix at that time point for the tree object. USER WARNING: this is still in development, and likely will not work all the time.

Matrix of the associations at given time

host_mu <- 1.0 # death rate
host_lambda <- 2.0 # birth rate
numb_replicates <- 1
time <- 1.0
symb_mu <- 0.2
symb_lambda <- 0.4
host_shift_rate <- 0.0
cosp_rate <- 2.0

cophylo_pair <- sim_cophyBD(hbr = host_lambda,
                           hdr = host_mu,
                           cosp_rate = cosp_rate,
                           host_exp_rate = host_shift_rate,
                           sdr = symb_mu,
                           sbr = symb_lambda,
                           numbsim = numb_replicates,
                           time_to_sim = time)
time <- 1.0
assoc_mat_at_t <- get_assoc(t=time, tr_pair_obj = cophylo_pair[[1]])