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Parities And Correspondence

Bijux Phylogenetics is compared with established phylogenetic software at explicit, reviewable boundaries. The comparison may be a live call to an R package, a checked reference fixture, a benchmark against a named implementation, or an adapter that executes an external engine. Those are different relationships and the documentation keeps them separate.

flowchart LR
    question["Named scientific<br/>operation"]
    bijux["Bijux result"]
    reference["Live tool or<br/>checked fixture"]
    normalize["Aligned inputs,<br/>units and conventions"]
    compare["Declared fields<br/>and tolerances"]
    outcome["Passed · failed<br/>or skipped case"]

    question --> bijux
    question --> reference
    bijux --> normalize
    reference --> normalize
    normalize --> compare --> outcome

Decide Whether You Need Execution Or Comparison

Start from the claim you need to make:

Needed claim Correct record Example conclusion
a named external tool can run inside a Bijux workflow adapter execution IQ-TREE2 executed with this input, command, version, and accepted native output
Bijux can read an existing external artifact parser record this BEAST or MrBayes artifact satisfies the supported parse contract
two implementations agree for one operation parity case aligned observations for this registered case satisfy the declared rules
correspondence supports a scientific statement Evidence Book claim the current bounded claim has the recorded verdict and limitations

These records can share files but they answer progressively different questions. Running IQ-TREE2 through an adapter is not a comparison with native Bijux inference. Parsing the same tree shape is not evidence that likelihoods or support estimands agree. Choose the claim first so a successful execution is not reported as a stronger correspondence result.

Reference Landscape

Relationship Tools What the repository owns What that record does not establish
live R parity APE, GEIGER, phytools governed cases, R runners, normalization, tolerances, mismatch artifacts package-wide interchangeability or unselected operations
checked R-derived correspondence nlme, selected course workflows and fixtures frozen inputs/outputs, comparison rules, provenance and limits a current live execution of the reference package
external alignment and tree execution MAFFT, trimAl, IQ-TREE2, FastTree adapters, configuration, execution capture, parsing and normalized artifacts that Bijux owns or independently reproduces the external algorithm
external posterior execution and review MrBayes, BEAST preparation, execution adapters, trace/tree parsing, diagnostics and reports posterior agreement without a separate aligned comparison

An adapter is not automatically a parity proof. It establishes that the external program can participate in a governed Bijux workflow. Numerical or structural equivalence requires a separate comparison with aligned assumptions and explicit observation rules.

Name The Kind Of Correspondence

“Parity” is too broad without the relationship being tested. One case can establish several layers, but a stronger layer requires its own observations.

Relationship Question Minimum evidence Does not establish
invocation can the named reference operation be selected and executed? versions, command/call, inputs, terminal state comparable outputs
structural do both outputs contain the same keyed objects and shapes? taxa, nodes, parameters, dimensions, order and omissions numerical agreement
numerical do aligned values satisfy declared exact or tolerance rules? structural identity, both values, rule, complete denominator identical failure behavior or scientific adequacy
stochastic distribution do sampled outputs satisfy registered distributional or calibration rules? seed/chain/replicate populations, statistic and threshold draw-wise identity or universal convergence
behavioral do validation, defaults, refusals, status and artifact semantics support the same consumer contract? input and failure corpus plus interface observations package-wide substitutability
scientific claim does the correspondence support one bounded interpretation? claim dependency, source, observations, verdict, limits and freshness transfer to another study or estimand

Report the strongest relationship actually observed. A numerically matching scalar does not imply behavioral equivalence, while a structurally matching tree can still contain different branch lengths, support meanings, or likelihood conventions.

Choose The Relationship From The Question

Question Required relationship Minimum retained record
Does one registered operation agree with APE, GEIGER, or phytools in this environment? live R parity case tool versions, case identity, both outputs, normalization, observations, tolerance, status
Does Bijux reproduce a frozen reference result without R? checked-fixture correspondence fixture provenance, frozen output identity, Bijux output, comparison rule
Can an external executable participate in a governed workflow? external-engine adapter execution executable version, invocation, streams, native files, parser result, workflow status
Does one native result agree with an external engine? explicit cross-engine comparison aligned models, inputs, meanings, observations, tolerances, both denominators
Does repository evidence support a bounded study claim? Evidence Book bundle claim ID, source, inputs, execution, checks, observations, verdict, freshness

One run can contribute to several records, but it does not merge their status names. Select the relationship before choosing a command or interpreting a green result.

Correspondence Is Not Substitutability

Two surfaces can agree on selected observations while remaining unsuitable as drop-in replacements. A substitution claim needs a broader contract than a numerical parity claim.

Dimension Correspondence asks Substitution additionally requires
input were the selected scientific objects aligned? accepted formats, validation, defaults, missing-data policy, and refusal behavior align for intended users
method were the compared estimands and parameterizations aligned? the replacement exposes every required model, constraint, and configuration
result did registered observations satisfy their rules? result fields, ordering, units, uncertainty, omissions, and status semantics remain usable
operation did the selected case execute? failure, retry, resource, concurrency, and artifact behavior satisfy the consuming workflow
assurance is the named case supported? coverage and independent evidence match the full intended substitution scope

The repository publishes operation-scoped correspondence. Unless a specific consumer contract says otherwise, a passing case does not authorize replacing APE, GEIGER, phytools, MAFFT, IQ-TREE2, BEAST, or another owner across an analysis pipeline.

Three Records, Three Meanings

Record Status owner What it establishes
parity harness case live or checked-fixture runner: passed, failed, skipped whether one registered case executed and satisfied its comparisons
external-engine bundle adapter and workflow result state whether a named external computation was prepared, executed, parsed, or refused
Evidence Book bundle governed verdict vocabulary whether identified scientific claims matched, mismatched, or remained non-comparable

These records may be linked but are not interchangeable. A skipped R case has no Evidence Book verdict. A successful adapter run is not a parity case. An open follow-through item describes remaining resolution work; it does not replace a bundle's recorded verdict.

Reading Paths

The Public Contract

Every parity claim names the external tool and version, Bijux surface, fixture, parameterization, compared fields, tolerance, execution mode, and case status. Unavailable R packages and unsupported reference cases remain visible as skips or out-of-scope boundaries rather than being counted as passes.

A complete claim can be read as:

For operation, Bijux version and surface was compared with reference version and surface on fixture or corpus, after normalization, using observations and rules. Of selected cases, passed, failed, and skipped counts were retained at artifact location. The conclusion is limited to named scope.

Omitting the denominator, reference identity, or comparison rule turns a reviewable correspondence statement into an unverifiable similarity claim.