<scp>tRophicPosition</scp>, an<scp>r</scp>package for the Bayesian estimation of trophic position from consumer stable isotope ratios
Bibliographic record
Abstract
Abstract Stable isotope analysis provides a powerful tool to identify the energy sources which fuel consumers, to understand trophic interactions and to infer consumer trophic position (TP), an important concept that describes the ecological role of consumers in food webs. However, current methods for estimating TP using stable isotopes are limited and do not fulfil the complete potential of the isotopic approach. For instance, researchers typically use point estimates for key parameters including trophic discrimination factors and isotopic baselines, and do not explicitly include variance associated with these parameters when calculating TP. We present “tRophicPosition,” anrpackage incorporating a Bayesian model for the calculation of consumer TP at the population level using stable isotopes, with one or two baselines. It combines Markov Chain Monte Carlo simulations through JAGS and statistical and graphical analyses using R. We model consumer and baseline observations using relevant statistical distributions, allowing them to be treated as random variables. The calculation of TP—a random parameter—for one baseline follows standard equations linking15N enrichment per trophic level and the trophic position of the baseline (e.g. a primary producer or primary consumer). In the case of two baselines, a simple mixing model incorporating δ13C allows for the differentiation between two distinct sources of nitrogen, thus including heterogeneity derived from alternatives sources of δ15N. Methods currently implemented in “tRophicPosition” include loading, plotting and summarizing stable isotope data either from multiple sites and/or communities or a local assemblage; loading trophic discrimination factors from an internal database or generating them; defining and initializing a Bayesian model of TP; sampling posterior parameters; analysing, comparing and plotting posterior estimates of TP and other parameters; and calculating a parametric (non‐Bayesian) TP estimate. Additionally, full documentation including examples, multiple vignettes and code are available for download.
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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 | 0.007 | 0.028 |
| Meta-epidemiology (narrow) | 0.005 | 0.003 |
| Meta-epidemiology (broad) | 0.004 | 0.005 |
| Bibliometrics | 0.004 | 0.003 |
| Science and technology studies | 0.001 | 0.002 |
| Scholarly communication | 0.004 | 0.003 |
| Open science | 0.005 | 0.004 |
| Research integrity | 0.002 | 0.005 |
| Insufficient payload (model declined to judge) | 0.196 | 0.123 |
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".