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Cluster bootstrap for pairwise host-sharing models

Source: R/cluster_bootstrap_phylopred.R
cluster_bootstrap_phylopred.Rd

Nonparametric bootstrap that resamples whole parasites (clusters) with replacement and refits the logistic regression on each replicate. This respects the non-independence of rows that share a parasite in a prepare_pair_data data set, unlike a naive row-level bootstrap. When a group column is present, resampling is stratified within groups and the model includes a group-by-distance interaction.

Usage

cluster_bootstrap_phylopred(
  pairs,
  n_boot = 1000,
  seed = NULL,
  conf_level = 0.95
)

Arguments

pairs

A data.frame from prepare_pair_data.

n_boot

Integer. Number of bootstrap replicates. Default 1000.

seed

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

conf_level

Confidence level for percentile intervals. Default 0.95.

Value

An object of class "phylopred_cluster_bootstrap", a list with:

draws

Matrix of bootstrap coefficient draws (replicates x terms).

estimates

Coefficients of the model fitted to the full data.

confidence_intervals

Percentile confidence intervals per term.

n_boot, seed, conf_level

Bootstrap settings.

See also

prepare_pair_data, compare_phylopred_slopes

Examples

# Three parasites keep the example fast
top <- names(sort(table(beetleTreeInteractions[[1]]),
                  decreasing = TRUE))[1:3]
sub <- beetleTreeInteractions[
  as.character(beetleTreeInteractions[[1]]) %in% top, ]
pairs <- prepare_pair_data(sub, phy_dist)
#> Warning: 5 interaction record(s) dropped: host not in 'phydist'.
cluster_bootstrap_phylopred(pairs, n_boot = 5, seed = 42)
#> Phylopred cluster bootstrap (5 replicates)
#>             estimate    2.5%   97.5%
#> (Intercept)  -0.6507 -0.7935 -0.6153
#> phydist      -0.0007 -0.0013 -0.0003