Bootstrap a phylopred logistic regression model — bootstrap_phylopred_model • phylopred

Runs the phylopred logistic regression n times using random focal host sampling, returning a distribution of coefficient estimates.

Usage

bootstrap_phylopred_model(incidence, phydist, n = 1000, seed = NULL)

Arguments

incidence: A binary incidence matrix (rows = parasites, cols = hosts).
phydist: A square, numeric phylogenetic distance matrix among hosts.
n: Integer. Number of bootstrap iterations. Default 1000.
seed: Integer or NULL. Random seed for reproducibility. Default NULL.

Value

An S3 object of class "phylopred_bootstrap", a list with:

call: The matched call.
n: Number of bootstrap iterations.
seed: The seed used.
coefficients: A matrix of n rows x 12 columns (coefficient info from each iteration).
summary: A data.frame with the column-wise means (same 12 columns).
metadata: List with n_parasites and n_hosts.

See also

fit_phylopred_model, predict_phylopred_probability

Examples

incidence <- prepare_incidence_matrix(beetleTreeInteractions)
aligned   <- align_phylopred_inputs(incidence, phy_dist)
bootstrap_phylopred_model(aligned$incidence, aligned$phydist, n = 5, seed = 42)
#> Phylopred bootstrap (5 iterations)
#> Intercept (mean): -1.6305
#> Slope     (mean): -0.0016