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est-data-analysis

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Use when executing and reporting the analysis for an Environmental Science & Technology (ES&T) manuscript so it survives expert review — analytical QA/QC, honest uncertainty, statistics appropriate to environmental data, and closed mass balances. It guides analysis and reporting norms; it does not fabricate results.

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Source SKILL.md: https://github.com/brycewang-stanford/Awesome-Journal-Skills/blob/HEAD/Environmental-Science-and-Technology-Skills/skills/est-data-analysis/SKILL.md

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Data Analysis (est-data-analysis)

ES&T reviewers scrutinize the analytical chain: blanks, recoveries, detection limits, replicates, and whether the numbers add up. This skill covers execution and reporting; design decisions live in est-study-design, and deposit/reproducibility in est-reporting-and-reproducibility.

When to trigger

  • Reducing raw instrument/field data into results
  • Building the results section and the QA/QC reporting
  • A reviewer asked about detection limits, recoveries, replicates, or statistics
  • Closing a mass/energy balance or fitting kinetics/dose–response

Analysis norms ES&T expects

  1. Report QA/QC explicitly. Method/field blanks, matrix-spike recoveries, CRM results, LOD/LOQ, calibration range and R², surrogate/internal-standard recoveries, and how non-detects were handled.
  2. Honest uncertainty. Report replicates with measures of dispersion (SD/SE/CI), not single values; propagate uncertainty through derived quantities; state n every time.
  3. Right statistics for environmental data. Handle left-censored (below-LOD) data correctly (e.g., substitution caveats, MLE/ROS, Kaplan–Meier); check distributional assumptions; use nonparametric or transformed analyses for skewed/heteroscedastic data; correct for multiple comparisons.
  4. Mass / energy balance. Account for products, sorbed and volatilized fractions, and losses; report closure (%) and explain gaps.
  5. Kinetics / dose–response. Report rate constants/half-lives with CIs and goodness of fit; EC/IC/LC values with confidence bounds; state the model fitted.
  6. Effect size & significance. Give magnitudes and intervals, not p-values alone; relate results to environmentally meaningful thresholds.

Reproducibility while you work (not at the end)

  • A master script/workflow regenerates every figure, table, and SI exhibit from processed data.
  • Set and report seeds for any stochastic step (bootstrap, Monte Carlo, simulation).
  • Pin software/package versions; record instrument settings and integration parameters.
  • Keep figure/table numbers matched to script outputs (see est-reporting-and-reproducibility).

QA/QC reporting table reviewers expect to see

ES&T referees often work down a mental analytical checklist. Reporting each item pre-empts the most common "rigor not established" objection. The minimum set, with what a reviewer reads when it is absent:

ElementWhat to reportIf omitted, the reviewer assumes
Method/field blanksblank levels vs. sample levels; subtraction approachcontamination is uncontrolled
Recoveriesmatrix-spike % and CRM agreementquantitation is biased/unknown
LOD/LOQderivation (e.g., 3σ/10σ or S/N) and per-analyte values"detections" may be noise
Calibrationrange, R², whether samples fall in rangeextrapolation beyond standards
Surrogate/IS recoveriesper-sample recovery correctionrun-to-run drift hidden
Non-detectscensoring method (ROS/MLE/KM), not bare substitutionsummary statistics distorted

Worked micro-example (illustrative — PFAS quantitation with censored data)

A river-PFAS dataset (illustrative numbers) shows how the rules combine into a reportable result:

  • 24 samples, triplicate injection; LOQ for PFHxA = 0.5 ng/L (illustrative, derived at 10×S/N).
  • Matrix-spike recovery 92% (RSD 7%, n=6); field blank < LOQ; surrogate-corrected.
  • 9 of 24 below LOQ — left-censored. Naive half-LOQ substitution would report a mean of 3.1 ng/L; regression-on-order-statistics (ROS) gives 2.4 ng/L (illustrative), because substitution inflated the low tail. Report the ROS mean with its CI and state the method.
  • Reported result: "PFHxA = 2.4 ng/L (95% CI 1.7–3.3, n=24, 38% < LOQ; ROS), recovery 92±7%." That single line carries magnitude, uncertainty, n, censoring handling, and recovery — the form a reviewer can sign off without a query.

Referee-pushback patterns and the venue-specific fix

  • "Detection limits and QA/QC are not reported." → Add the blank/recovery/LOD/LOQ table to the SI and cite it from Methods; never leave it implicit.
  • "Below-detect data handled by substitution." → Re-analyze with ROS/MLE/Kaplan–Meier; show the result is robust to the censoring choice.
  • "The mass balance does not close." → Report closure %, name the unaccounted fraction (sorbed, volatilized, mineralized), and bound it rather than ignoring the gap.

Anti-patterns

  • Results with no blanks, recoveries, or detection limits reported
  • Single measurements with no replication or dispersion
  • Naive zero/half-LOD substitution for heavily censored data with no caveat
  • A transformation/treatment study whose mass balance never closes (or is never reported)
  • p-values without effect sizes or environmental thresholds
  • Over-fitting kinetics/dose–response with too few points

Output format

【Main result】magnitude + uncertainty (n, SD/CI) + units
【QA/QC】blanks / recoveries / CRM / LOD-LOQ / calibration reported? [Y/N]
【Censored data】handled how
【Mass/energy balance】closure % + explanation
【Statistics】appropriate test + assumptions checked? [Y/N]
【Reproducible】master script + seeds + pinned versions? [Y/N]
【Next】est-figures-and-tables

Supplementary resources