predict phylosem — predict.phylosem • phylosem

extract the predictive mean and covariance for nodes or tips based on names from tree, x$tree$tip.label and x$tree$node.label

Usage

# S3 method for class 'phylosem'
predict(
  object,
  taxon,
  what = c("p_g"),
  se.fit = TRUE,
  include_fixed = TRUE,
  ...
)

Arguments

object: Output from phylosem
taxon: vector of taxon names (matched against tree) to predict traits
what: What output to calculate (currently only the linear predictor is supported)
se.fit: Whether to report predictive covariance, where sqrt(diag(pred$cov)) is the standard errors
include_fixed: Whether to include uncertainty in fixed effects when calculating predictive covariance
...: Not used

Value

When se.fit = FALSE, it returns a matrix of predicted traits (rows) by taxon (column). When se.fit = TRUE, it returns a list:

est: matrix of predicted traits
cov: array of predictive covariance among traits (1st and 2nd dims) by taxon (3rd dim)