smooth_pvalues: Hierarchical correction of p-values
In abichat/zazou: Z-Scores As Ornstein-Uhlenbeck

Description Usage Arguments Value Examples

Hierarchical correction of p-values

smooth_pvalues(
  pvalues,
  esign = NULL,
  tree,
  arg_shiftpunct = list(alphaOU = 1, method = "scaled lasso"),
  arg_shiftconf = list(alpha_conf = 0.05, method = "score system")
)

`pvalues`	Vector of p-values.
`esign`	Vector of e-signs (optional).
`tree`	Tree, as a `phylo` object.
`arg_shiftpunct`	Arguments to be passed to `estimate_shifts` function.
`arg_shiftconf`	Arguments to be passed to `estimate_confint` function.

A corrected vector.

pval_obs <- test_kruskalwallis(chlamydiae$X, chlamydiae$Y)$p.value
tree <- force_ultrametric(chlamydiae$tree)
smooth_pvalues(pvalue = pval_obs, tree = tree,
               arg_shiftpunct = list(alpha = c(0.1, 2),
                                     method = "scaled lasso"))