Fit a phylopred logistic regression model

Fits a logistic regression model relating host susceptibility to phylogenetic distance.

Usage

fit_phylopred_model(incidence, phydist, seed = NULL)

Arguments

incidence

A binary incidence matrix (rows = parasites/pathogens, cols = hosts).

phydist

A square, numeric phylogenetic distance matrix among hosts. Row/col names must match the column names of incidence.

seed

Integer or NULL. Random seed for reproducibility. Default NULL.

Value

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

call

The matched call.

coefficients

Named numeric vector c(intercept, slope).

standard_errors

Named numeric vector c(intercept, slope).

confidence_intervals

Matrix with rows c("intercept","slope") and cols c("2.5%","97.5%").

fitted_model

The underlying glm object.

training_data

The data.frame used for model fitting.

convergence

Logical; whether the GLM converged.

metadata

List with n_parasites, n_hosts, and seed.

See also

bootstrap_phylopred_model, predict_phylopred_probability

Examples

incidence <- prepare_incidence_matrix(beetleTreeInteractions)
aligned   <- align_phylopred_inputs(incidence, phy_dist)
fit_phylopred_model(aligned$incidence, aligned$phydist, seed = 42)
#> Phylopred model
#> Intercept: -1.2397 (SE: 0.1791)
#> Slope:     -0.0025 (SE: 0.0004)
#> Convergence: TRUE