% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/sequence-analysis-audit.R
\name{compare_sequence_analysis_results}
\alias{compare_sequence_analysis_results}
\title{Compare two gp3sequences analysis results}
\usage{
compare_sequence_analysis_results(
  x,
  y,
  tolerance = 1e-08,
  compare_values = FALSE
)
}
\arguments{
\item{x, y}{Two analysis objects.}

\item{tolerance}{Numerical comparison tolerance.}

\item{compare_values}{Logical; when \code{TRUE}, also run \code{all.equal()} on the
complete objects after structural comparison.}
}
\value{
An object of class \code{gp3_sequence_analysis_comparison} containing
per-field comparisons, both audits, optional whole-object comparison, and
an overall equality flag.
}
\description{
Compares structural contracts and recoverable provenance from two analysis
objects. This helper is intended for regression checks, sensitivity analyses,
and reproducibility audits; it does not select a statistically or
substantively "best" analysis.
}
\examples{
sequences <- data.frame(
  sequence_id = rep(c("s1", "s2", "s3"), each = 3L),
  sequence_order = rep(1:3, times = 3L),
  state = c(
    "A", "B", "C",
    "A", "B", "B",
    "C", "B", "A"
  )
)
d1 <- compute_sequence_distance(
  sequences,
  method = "levenshtein"
)
d2 <- compute_sequence_distance(
  sequences,
  method = "levenshtein"
)
compare_sequence_analysis_results(d1, d2)

}
