Change: Import legacy su2013establishment manuscript

Authors
Affiliations

Ming Su

Key Laboratory of Environmental Aquatic Chemistry, State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences.

University of Chinese Academy of Sciences.

Virginie Gaget

South Australia Water Corporation, Australian Water Quality Centre

Ecology, Evolution and Landscape Sciences, School of Earth and Environment Sciences, Adelaide University

Steven Giglio

South Australia Water Corporation, Australian Water Quality Centre

Healthscope Pathology SA

Michael Burch

South Australia Water Corporation, Australian Water Quality Centre

Wei An

Key Laboratory of Environmental Aquatic Chemistry, State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences.

Min Yang

Key Laboratory of Environmental Aquatic Chemistry, State Key Laboratory of Regional Environment and Sustainability, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences.

University of Chinese Academy of Sciences.

Published

September 4, 2026

Change log

Purpose

Import the curated final-submission sources from ../su2013establishment_old into the current Quarto manuscript workflow.

Changes

  • Converted lastsubmit/Manuscript.tex into the active manuscript sections.

  • Converted Supporting_v130114.tex (cross-checked against lastsubmit/Supporting.tex) into MS/SM.qmd, covering all six supplementary subsections: field sites, geosmin component table, primer specificity (ARG/GSG gels), field-sample validation ANOVA, extracellular geosmin vs. GSG regression, and ARG/GSG field-sample comparison. Prose and strain-count wording follow the final lastsubmit version where it corrects the earlier draft (e.g. “30 Anabaena strains and 17 other strains”, hyphenated FADC-0001/FADC-0002); the geosmin-component table keeps the earlier version’s unrounded decimal values.

  • Copied the selected legacy manuscript package into input/legacy/.

  • Copied historical data into data/raw/legacy/ and figure assets into figures/legacy/; all figures referenced by SM.qmd (samplingsite, Gel_ARG, Gel_GSG, arganova, gsganova, GSGCompare_OUT, fieldvar) are present under figures/.

  • Updated project metadata and bibliography.

  • Added project truth, decision, result, and handoff notes.

  • Added a figure-claim map and a base-R legacy input preflight.

  • Fixed a project-wide crossref bug: 29 instances across MS_methods.qmd (5), MS_results.qmd (15), and SM.qmd (9) wrote a literal “Figure”/ “Table”/“Equation” immediately before a @fig-/@tbl-/@eq- reference, duplicating the prefix that pandoc-crossref already inserts (rendered as “Figure Fig. 2”, “Table Table 1”, etc. — confirmed in the previously rendered www/MS/MS.pdf). Removed the redundant literal word everywhere; re-rendered MS.pdf and SM.pdf confirm the duplication is gone.

  • Renamed all 58 citation keys in BB/localRef.bib (and every citing .qmd file) to Ming’s standard key format (lastname+year+firstwordoftitle, lowercase), matching each entry against /Users/ming/literature/Ref.bib by DOI then by normalized title. This also resolved the 19 “no DOI match” entries from the earlier reference audit — all 19 exist in the personal library, they just hadn’t matched on DOI alone. See notes/reference_audit.md and notes/decision_log.md.

Limitations

The analysis script (input/legacy/data/DataAnalysis.R) remains unrefactored. Citation syntax still reflects rendered author-year prose.

Verification