Think like a Bayesian and avoid pitfalls from our frequentist past
Bibliographic record
Abstract
Bayesian inference is a powerful tool that is increasingly being used by ecologists. This is largely due to the flexibility in model specification and improvements in software that makes this tool easier to use. However, with increasing ease of use comes a risk of misuse or abuse. We review four major issues we have identified in the use of Bayesian methods and offer reminders and suggestions that will improve the application and reporting of Bayesian inference while at the same time, hopefully, avoiding the pitfalls that have plagued null hypothesis statistical testing (NHST). These issues include; 1) understanding software and model specification; 2) use of prior probability distributions; 3) maximizing utility of posterior probability distributions; and 4) avoiding dichotomous thinking (i.e., the NHST pitfall). We suggest ecologists should strive for openness in their use of statistical software by understanding their model and providing the full computer code used, develop reasonable and informative priors, and make full use of posterior information that Bayesian methods provide. At the same time, ecologists should avoid dichotomizing results into significant/ non-significant boxes, eliminate null hypothesis tests (including probability intervals for hypothesis testing), and use clear language when describing results. Finally, quantitative training should be expanded in undergraduate curricula to provide students with a larger suite of foundational core concepts that extend beyond NHST.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.073 | 0.248 |
| Meta-epidemiology (narrow) | 0.002 | 0.002 |
| Meta-epidemiology (broad) | 0.002 | 0.002 |
| Bibliometrics | 0.006 | 0.004 |
| Science and technology studies | 0.004 | 0.016 |
| Scholarly communication | 0.013 | 0.033 |
| Open science | 0.006 | 0.005 |
| Research integrity | 0.007 | 0.017 |
| Insufficient payload (model declined to judge) | 0.011 | 0.007 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".