Additional file 3 of Large-diameter trees and deadwood correspond with belowground ectomycorrhizal fungal richness
Bibliographic record
Abstract
Additional file 3: Figure S1. The distribution of fungal sequence count for soil samples taken at the Utah Forest Dynamics Plot, Utah, USA. The red horizontal line denotes the 12,500 sequence cutoff used to rarefy the sequence abundances. Figure S2. The interpolated mineral soil nutrients at the Utah Forest Dynamics Plot, Utah, USA. Figure S3. A principal coordinate analysis (PCA) of soil nutrients at the Utah Forest Dynamics Plot, Utah, USA. Soil nutrients were interpolated across the plot and the values at 117 sampling locations were used for this PCA. Figure S4. The diameter at breast height (1.37 m; cm) for all tree species with > 10 individuals at the Utah Forest Dynamics Plot, Utah, USA. Figure S5. The distribution of (A) observed fungal amplicon sequence variants (ASVs) and (B) Shannon’s Alpha diversity for soil samples taken at the Utah Forest Dynamics Plot, Utah, USA. The red horizontal lines in each panel mark the mean value. Figure S6. The species accumulation curves for all fungal amplicon sequence variants (ASV) (a), ectomycorrhizal fungi (b), and saprotrophic fungi (c) at the Utah Forest Dynamics Plot, Utah, USA. Figure S7. A fitted variogram of the semi-variance of the depth of the LFH layer (litter + duff) from 295 measurements across the Utah Forest Dynamics Plot, UT, USA. Figure S8. The estimated age of the forest at the Utah Forest Dynamics Plot, Utah, USA. Tree age was estimated using kriging interpolation of 127 trees. Figure S9. The increase in mean square error (a) and partial dependence plots (b) from a random forest model assessing the influence of the nearest large (>40.2 cm diameter at breast height) tree species on total fungal species richness at the Utah Forest Dynamics Plot, Utah, USA. Figure S10. The increase in mean square error (a) and partial dependence plots (b) from a random forest model assessing the influence of the nearest large (>40.2 cm diameter at breast height) tree species on saprotrophic fungal species richness at the Utah Forest Dynamics Plot, Utah, USA.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
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 | 0.001 | 0.023 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.002 | 0.004 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.002 | 0.003 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.885 | 0.211 |
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".