agsy-figures-and-tables - SKILL.md Agent Skill

name: agsy-figures-and-tables description: Use when building figures and tables for an Agricultural Systems (AgSy) manuscript so exhibits communicate interactions, dynamics, trade-offs, and model performance clearly. AgSy is a systems journal, so the best exhibits show trade-off frontiers, observed-vs-simulated fit, resource flows, and conceptual system diagrams — not just a bar chart of one treatment. Designs exhibits; it does not run the analysis.

Figures & Tables (agsy-figures-and-tables)

Exhibits are where a systems reviewer checks whether the model and the trade-offs are real. At AgSy the strongest exhibits make interactions, dynamics, and trade-offs visible, and let a reader judge model performance at a glance. A wall of single-treatment bar charts does not belong in a systems paper.

When to trigger

Designing the main results figure or a key model-performance exhibit
Deciding what belongs in the article vs. supplementary material
A reviewer found an exhibit unclear, mislabeled, or not self-contained
Presenting scenario comparisons or trade-offs

Principles

Self-contained. A reader should understand each exhibit from its caption, axis/column labels, and note alone. State units, system level (field/farm/landscape/region), scenario, N, and time horizon.
Show the system, not one factor. Prefer exhibits that reveal interactions and trade-offs:
- Trade-off / Pareto-front plots (e.g., profit vs. N leaching across options)
- Observed-vs-simulated (1:1) plots with fit statistics (RMSE/NSE/bias) for model evaluation
- Time series of state variables to show dynamics and feedbacks
- Sankey / flow diagrams for resource, nutrient, or energy flows
- Conceptual system diagrams (boxes/arrows) for boundaries and components
- Multi-indicator / radar profiles for sustainability comparisons
Show uncertainty. Intervals, ensemble ranges, or boxplots — not bare point estimates from a single model run.
Accessible. Colorblind-safe palettes; legible in grayscale; no chartjunk or 3D; vector output (PDF/EPS) for print.
Reproducible. Each exhibit is generated by the master workflow; numbers match the deposited data/code/model exactly (see agsy-reproducibility-and-data-policy).

Article vs. supplementary

Keep the few exhibits that carry the systems argument (trade-offs, key dynamics, model fit) in the article; move full calibration tables, parameter lists, and exhaustive scenario grids to supplementary material.

Pick the exhibit from the claim (illustrative)

A crop–livestock simulation has four candidate main figures; choose by what the systems claim needs:

Claim is "the model is credible" → observed-vs-simulated 1:1 plot with RMSE/NSE/bias on the figure.
Claim is "there is a trade-off" → Pareto front of gross margin vs. N surplus across options, with the recommended region marked — not a scenario bar chart that hides the frontier.
Claim is "feedbacks drive the result" → time series of state variables (herd, manure N, rotation) showing the loop, with an ensemble band for uncertainty.
Claim is "this is a system" → a conceptual boundary-and-components diagram, often the graphical abstract.

Referee pushback → the AgSy-specific fix

"The main figure is a single-treatment bar chart." → Replace it with a trade-off or 1:1 exhibit that shows interactions, not one factor.
"Fit is asserted, not shown." → Pair the observed-vs-simulated plot with the fit statistics on the same figure.
"No uncertainty on the headline result." → Add intervals, an ensemble band, or boxplots; one model run is not a result.

Anti-patterns

A single-treatment bar chart presented as the main result of a "systems" paper
Observed-vs-simulated shown without fit statistics, or fit statistics with no plot
Scenario tables that bury the trade-off instead of plotting the frontier
Point estimates from one model run with no uncertainty shown
Color-only encoding that fails in grayscale or for colorblind readers
Exhibit numbers/values that don't match the deposited model output

Operating pass for Agricultural Systems

Run this as a concrete capability pass. First lock the system boundary, actor decision, model/data linkage, and sustainability or food-security tradeoff; then test whether the manuscript addresses agricultural-systems reviewers who expect crop, farm, value-chain, environment, and policy components to be connected rather than listed.

Primary move: Return a claim-evidence-risk ledger; every recommendation must point to a manuscript location or missing artifact.
Decision ledger: return claim / evidence / blocker / next edit rows so the next pass can patch the manuscript directly.
Sibling comparison: compare against Field Crops Research for plot-level agronomy, Global Food Security for policy synthesis, Agricultural Economics for economics-first work; if the neighboring outlet has the stronger audience claim, recommend re-routing before polishing.
Verification floor: before submission-ready advice, re-open resources/official-source-map.md for volatile rules and name the one unresolved fact that could change the recommendation.

Output format

【Main exhibit】what system interaction / trade-off / fit it shows
【Type】trade-off frontier / 1:1 / time series / flow diagram / system diagram / radar
【Self-contained?】caption + labels + units + level + scenario + N? [Y/N]
【Uncertainty shown?】intervals / ensemble / boxplot? [Y/N]
【Article vs supplementary】split decided
【Reproducible?】generated by master workflow, matches package? [Y/N]
【Next】agsy-writing-style

Supplementary resources

../../resources/external_tools.md — plotting, flow-diagram, and mapping tools for systems exhibits
../../resources/official-source-map.md — Highlights / graphical-abstract requirements