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Joint confidence ellipse for intercept and slope

Source: R/phylopred_confidence_ellipse.R
phylopred_confidence_ellipse.Rd

Computes the boundary of the joint confidence region ("ellipse") for a pair of coefficients, either from a fitted glm (using the asymptotic covariance matrix) or from a cluster_bootstrap_phylopred object (using the empirical covariance of the bootstrap draws, which respects parasite-level clustering).

Usage

phylopred_confidence_ellipse(
  object,
  terms = c("(Intercept)", "phydist"),
  level = 0.95,
  n_points = 200
)

Arguments

object

A glm fit or a phylopred_cluster_bootstrap object.

terms

Character vector of length 2 with the coefficient names. Default c("(Intercept)", "phydist").

level

Confidence level. Default 0.95.

n_points

Number of points on the ellipse boundary. Default 200.

Value

A data.frame with n_points rows and two columns named after terms, tracing the ellipse boundary. The center (point estimates) is returned as the "center" attribute.

See also

cluster_bootstrap_phylopred

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'.

# From a glm: asymptotic ellipse
fit <- glm(suscept ~ phydist, data = pairs, family = binomial())
ell <- phylopred_confidence_ellipse(fit)
plot(ell, type = "l")
points(t(attr(ell, "center")), pch = 19)

# From a cluster bootstrap
boot <- cluster_bootstrap_phylopred(pairs, n_boot = 5, seed = 42)
ell_b <- phylopred_confidence_ellipse(boot)
lines(ell_b, lty = 2)