Skip to content

Bijux Pollenomics Product Guide

bijux-pollenomics is the product guide for the repository's public evidence. It explains what the repository publishes today, why those outputs exist, how far they can be trusted, and where to go next without reading the source code first.

The central idea is simple. This repository rebuilds one governed evidence system, then publishes several public-facing cuts from that same state. Pollen context, environmental archaeology, boundary framing, fieldwork records, and animal ancient-DNA recovery all live in one repository, but they do not all carry the same scientific weight. This guide explains those differences directly instead of leaving them buried in the file tree.

That same model now includes the Sweden lake evidence program. The lake packet is not a side spreadsheet pasted beside the atlas. It is another published cut through the repository evidence state, with its own ranking logic, shortlist rules, and honesty boundaries.

Use this handbook when your first question is:

  • what this repository is actually for
  • what I can use from it right now
  • what kind of question each output can answer
  • what the current limits are before I rely on a public map, report, or data file

Do not use this handbook when you need maintainer-only release policy, internal governance, or package-check implementation details. Those belong in the repository's internal docs, not on the public product surface.

Open the documentation home What this repository is for How evidence becomes outputs Commands and public contracts Install and rebuild Checks and current limits

What You Can Learn Here

  • understand the product shape before reading package names or command syntax
  • decide whether you need the visible public answer, the narrower evidence chain, or the rebuild workflow behind it
  • tell which surfaces are mature public context and which remain partial or recovery-heavy
  • move from a big public question to the right page quickly instead of wandering through internal terminology

Publication Loop

flowchart TB
    sources["tracked source families"]
    normalization["normalization and review"]
    outputs["country bundles, report portal, and atlas surfaces"]
    readers["public user checks traceability and limits"]

    sources --> normalization
    normalization --> outputs
    outputs --> readers

What Most People Need First

  • what the repository already publishes with confidence: pollen context, environmental archaeology context, boundary framing, and governed report bundles
  • what the Sweden lake packet adds: candidate prioritization, scenario comparison, and a fieldwork shortlist without pretending those rankings replace field limnology
  • what remains visibly partial: animal ancient-DNA recovery and the claims that depend on deeper sample extraction
  • how to use the product without overstating it: start with public outputs for orientation, then drop to evidence and review surfaces when a claim matters
  • how this can grow to more countries and more regions: the world, Europe-plus, Nordic, and country outputs are meant to be one expansion model, not separate products

Start Here

  • start with foundation if you need the product answer: what this repository is for, what it refuses to claim, and why
  • move to architecture if you need the lifecycle answer: how evidence becomes reviewable files, reports, and maps
  • use interfaces if you need the runtime answer: which commands, files, and contracts are meant to stay stable
  • use operations if you need the practical answer: how to install, verify, rebuild, and recover locally
  • use quality if you need the trust answer: what the current checks, limits, and refusal rules actually say

Routes By Question

Evidence Routes

If your question is really about the evidence families behind the product, move from this handbook into the public data pages that explain them directly:

What This Guide Covers

  • the product shape of the runtime
  • the architecture that turns governed evidence into governed outputs
  • the public command and file contracts you can inspect
  • the operational route for rebuilding and checking the repository
  • the quality rules that keep visible output language honest
  • the places where ranking, atlas, and fieldwork outputs are informative but still narrower than a finished scientific inference engine

What This Guide Does Not Promise

  • that you already know the repository layout
  • that every visible output has the same scientific strength
  • that the current animal ancient-DNA slice already equals a finished pollenomics engine
  • that maintainer-only rules belong on the public product surface