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Compare host-sharing slopes between two clades

Source: R/compare_phylopred_slopes.R
compare_phylopred_slopes.Rd

Fits a single logistic regression with a group-by-phylogenetic-distance interaction to a pairwise data set built with prepare_pair_data and tests whether the slopes of the two groups differ. A more negative slope means the probability of sharing a parasite decays faster with phylogenetic distance, i.e. the clade is more of a phylogenetic specialist. Uncertainty for the slope difference comes from a parasite-level cluster bootstrap.

Usage

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

Arguments

pairs

A data.frame from prepare_pair_data with a group column containing exactly two groups.

n_boot

Integer. Number of cluster bootstrap replicates. Default 1000.

seed

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

conf_level

Confidence level. Default 0.95.

Value

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

groups

The two group labels (reference first).

slopes

Named vector with the slope of each group.

slope_difference

Slope of the second group minus the reference.

interaction_p_value

Wald p-value of the interaction term.

bootstrap

The cluster_bootstrap_phylopred object.

slope_cis

Bootstrap percentile CIs for each group's slope and for the difference.

fitted_model

The underlying glm object.

See also

prepare_pair_data, cluster_bootstrap_phylopred

Examples

# Compare Xyleborus beetles against other genera (subset kept small
# so the bootstrap example runs quickly)
parasites <- unique(as.character(beetleTreeInteractions[[1]]))
keep <- c(grep("^Xyleborus", parasites, value = TRUE)[1:3],
          parasites[!grepl("^Xyleborus", parasites)][1:3])
sub <- beetleTreeInteractions[
  as.character(beetleTreeInteractions[[1]]) %in% keep, ]
pairs <- prepare_pair_data(
  sub, phy_dist,
  group = function(x) ifelse(grepl("^Xyleborus", x), "Xyleborus", "other")
)
#> Warning: 4 interaction record(s) dropped: host not in 'phydist'.
compare_phylopred_slopes(pairs, n_boot = 5, seed = 42)
#> Phylopred slope comparison: Xyleborus vs other 
#> Slope Xyleborus: -0.0005  [-0.0006, -0.0003]
#> Slope other: -0.0010  [-0.0015, -0.0002]
#> Difference: -0.0006  [-0.0009, 0.0004]  (Wald p = 0.553)