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Effective statistics starts before you open a software package: define the question, design how data will answer it, inspect data quality, quantify uncertainty, test assumptions, and document every analytical decision. The ten rules below come from the 2016 PLOS Computational Biology editorial by Robert E. Kass, Brian S. Caffo, Marie Davidian, Xiao-Li Meng, Bin Yu, and Nancy Reid. They apply broadly to investigations in science, social science, engineering, digital humanities, and finance.

The authors stress that these are essential guidelines, not a replacement for years of statistical training. A statistician is most useful during planning, not only after data collection. As the editorial puts it, “Statistics is a language constructed to assist this process, with probability as its grammar.”

Use the ten rules as a workflow

The rules are connected. A well-posed question leads to an appropriate design; a sound design improves data quality; data quality and assumptions determine the analysis; uncertainty, replication, and reproducibility determine how much confidence others should place in the result.

The ten rules

  1. Let statistical methods answer the scientific question

    Start by asking what you need to learn, not “Which test should I use?” A study might seek to identify which genes differ between conditions, estimate an effect, predict future outcomes, describe a population, or discover groups. Those goals can call for different combinations of tests, plots, heat maps, clustering, regression, or other methods.

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    Bring statistical expertise into the project early enough to influence the question, measurements, sampling plan, and analysis—not merely to select a test after the experiment is finished. Sir Ronald Fisher’s warning, quoted in the editorial, is blunt: “To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination.”

  2. Remember that signals always come with noise

    Observed variation combines information relevant to your question with variation that obscures it. Probability models help describe that combination, estimate uncertainty, and distinguish random variation from systematic error (bias).

    More data does not automatically remove bias. The authors cite Google Flu Trends, which overestimated influenza prevalence by nearly 50%, largely because of data-collection bias. That is an illustration from their discussion, not a general error rate for big-data projects.

  3. Plan ahead—really ahead

    Before collecting consequential data, decide which outcome would answer the question and how you would interpret it. Specify, as far as practical:

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    • what will be measured and whether the measurement is valid;
    • which population or process the data should represent;
    • how observations will be sampled or assigned;
    • which sources of variation can be controlled;
    • what biases could enter through recruitment, measurement, or follow-up; and
    • how the planned analysis connects to the outcome.

    Planning also clarifies questions such as “What should my n be?” Sample size is meaningful only in relation to the outcome, design, expected variation, and precision or power required.

  4. Worry about data quality

    Understand the path from original observation to analysis. Verify units, variable definitions, coding of missing values, detection limits, duplicated records, outliers, and anomalies. Find out why values are missing; missingness caused by a particular group or condition can bias results.

    Use plots and simple summaries before fitting complex models. Exploration is valuable for finding errors and generating hypotheses, but selecting a result after extensive inspection changes how later inferential claims—especially p-values and intervals—should be interpreted.

  5. Analysis is more than computation

    Software executes algorithms; it does not decide whether an algorithm addresses your substantive question. Explain why the method fits the outcome, design, and data structure. Keep a structured record of data transformations, exclusions, model specifications, tuning choices, and outputs so another analyst can follow the same path.

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    A familiar menu option or default setting is not evidence that the resulting estimate is appropriate.

  6. Keep the approach as simple as the problem allows

    Begin with a parsimonious model and add complexity only when the design or evidence requires it. Simplicity improves interpretability and reduces opportunities for unstable estimates.

    It is not an absolute rule. Dependence among observations, many measurements, interactions, nonlinear processes, missing data, confounding, or sampling bias may require richer models. Good design often makes a simpler analysis defensible; a simple explanation should not conceal important structure.

  7. Report variability with the result

    An estimate without its uncertainty is incomplete. Depending on the design and model, report standard errors, confidence intervals, prediction intervals, or other suitable assessments of variation.

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    Account for dependence. Treating repeated measurements, clustered observations, family members, sites, batches, or time series as independent can make uncertainty appear much smaller than it is. Variation can also arise across days, laboratories, instruments, operators, or protocol changes; those sources belong in the design or analysis rather than being silently averaged away.

  8. Check the assumptions

    Every inference relies on assumptions, including methods sometimes advertised as “model-free.” Investigate whether assumptions about linearity, independence, measurement, sampling, and missing-data handling fit both the data and the real-world process.

    Examine model fit with relevant plots, including residual and data-structure diagnostics, and look for influential observations or systematic patterns. A model that passes a diagnostic does not become uniquely true; diagnostics identify serious incompatibilities and inform judgment.

  9. Replicate when possible

    Exploring many analyses and reporting only the attractive result can make ordinary inferential quantities look more convincing than they are. State how the analysis was developed, distinguish prespecified work from exploratory work, and avoid presenting data-driven selection as if it had been fixed in advance.

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    The most reliable response to data snooping is replication with new data, ideally by an independent investigator. When a full new study is impractical, perturbation or sensitivity analyses—such as changing reasonable preprocessing, specifications, or subsets—can reveal whether the finding is fragile. These checks do not replace replication.

  10. Make the analysis reproducible

    Reproducibility means that someone with the same data and a complete description of the analysis can recreate the tables, figures, and statistical inferences. Share data when legally and ethically possible, provide code and documentation, and record software versions, settings, random seeds, and computational environments.

    Reproducibility is different from independent replication. Reproduction re-runs the same evidence; replication tests whether a finding recurs with new data. The former is often achievable even when the latter is expensive or impossible.

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A practical pre-analysis checklist

  • Write the substantive question and the population or process it concerns.
  • Define the primary outcome, predictors, comparison, and estimand in plain language.
  • Document sampling, assignment, recruitment, measurement procedures, and likely bias.
  • Set rules for exclusions, missing values, transformations, and stopping where feasible.
  • Choose an analysis that matches the design and dependence structure.
  • Plan how uncertainty and important sources of variation will be reported.
  • Separate exploratory findings from confirmatory claims.
  • Specify diagnostics, sensitivity checks, and a route to new-data replication.
  • Preserve raw data, processing steps, code, package versions, and computational settings.

How to interpret a statistical result responsibly

Ask five questions before accepting a number:

  1. Does the estimate answer the original substantive question?
  2. Could selection, measurement, missingness, or sampling have introduced bias?
  3. How large is the uncertainty, and was dependence handled?
  4. Do diagnostics and subject-matter knowledge support the assumptions?
  5. Can another person reproduce the result, and does it recur in new data?

Treat statistics as a science rather than a recipe. Andrew Vickers’s phrase, quoted by the authors as a possible “Rule 0,” captures the attitude: “Treat statistics as a science, not a recipe.”

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Further reading

The editorial recommends Principles of Applied Statistics by D. R. Cox and C. A. Donnelly for readers who want a deeper treatment of planning investigations and drawing conclusions from data.

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