Unified Alpha Diversity Statistical Testing — test

One function for all alpha diversity statistical tests.

Usage

test_alpha(
  data.obj,
  test.type = c("difference", "trend", "volatility", "per_time"),
  alpha.name = c("shannon", "simpson", "observed_species"),
  alpha.obj = NULL,
  depth = NULL,
  subject.var = NULL,
  time.var = NULL,
  group.var = NULL,
  adj.vars = NULL,
  time.points = NULL,
  ...
)

Arguments

data.obj: A MicrobiomeStat data object containing feature.tab, meta.dat, and optionally feature.ann, tree, and feature.agg.list.
test.type: Type of test: - "difference": Test for group differences in alpha diversity - "trend": Test for temporal trends in alpha diversity - "volatility": Test for temporal instability in alpha diversity - "per_time": Test at each time point separately
alpha.name: Character vector. Alpha diversity indices to calculate. Options: "shannon", "simpson", "observed_species", "chao1", "ace", "pielou".
alpha.obj: Optional pre-calculated alpha diversity object.
depth: Rarefaction depth. NULL for no rarefaction.
subject.var: Character. Name of the subject/sample ID variable in meta.dat. Required for longitudinal and paired designs.
time.var: Character. Name of the time variable in meta.dat. NULL for cross-sectional studies.
group.var: Character. Name of the grouping variable (e.g., treatment, condition).
adj.vars: Character vector. Names of adjustment/covariate variables.
time.points: Time point specification. Can be: - NULL: use all available time points (auto-detect design) - Single value: cross-sectional at that time point - Vector of 2: paired design (baseline, followup) - Vector of >2: longitudinal with specific time points - List: list(baseline = "T0", followup = c("T1", "T2"))
...: Additional arguments passed to the underlying function.

Value

A list containing statistical results for each alpha diversity metric.

Examples

if (FALSE) { # \dontrun{
data(peerj32.obj)

# Cross-sectional test
test_alpha(peerj32.obj, "difference",
           alpha.name = c("shannon", "simpson"),
           group.var = "group")

# Longitudinal trend test
test_alpha(peerj32.obj, "trend",
           alpha.name = "shannon",
           subject.var = "subject",
           time.var = "time",
           group.var = "group")
} # }