Regional climate affects salmon lice dynamics, stage structure, and management
Bibliographic record
Abstract
REGIONAL CLIMATE AFFECTS SALMON LICE DYNAMICS, STAGE STRUCTURE, AND MANAGEMENT by Amy Hurford, Xiunan Wang, and Xiao-Qiang Zhao Contact: Amy Hurford, ahurford@mun.ca Several of these codes have dependencies on the PBSddesolve package. CODE TO MAKE FIGURES (have dependencies on *.Rdata files) (1) Figure1_map.R: makes FIGURE 1: Map and temperature and salinity plots (2) Figure2_R0Graphs.R makes FIGURE 2. This file calls Summary.Rdata, the output of R0Calcs.R. (3) Figure2_R0Calcs.R: performs the calculations underlying FIGURE 2. (4) Figure3_Dynamics: makes FIGURE 3. (5) Figure4_GenerationTime.R: makes FIGURE 4. (6) FigureS1_S2_ParamsFunc.R: makes FIGURES S1 & S2: Figure S.1 shows fits of functions for lab data describing life history parameters as a function of temperature and salinity. The output ParamsFunc.Rdata is called by subsequent codes. Figure S.2 examines evidence for local adaptation. (7) FigureS3_NumericalMethods.R: makes FIGURE S3. (8) SalinityMortalityCaligus.R: runs analyses for Caligus rogercresseyi adult mortality data shown in Figure S1. =============== DATA FILES (9) Data_Extraction.csv: The raw data extracted from the sources as listed in Section S1 of Hurford et al. Site abbreviations are described in detail in Section S1 of Hurford et al. (10) CH.Rdata: Parameters and data for the site in Chile (CH). This file is called by other codes. (11) IM3.Rdata: Parameters and data for the site a site off the coast of Ireland (IM3). (12) IM4.Rdata: Parameters and data for the site a site off the coast of Ireland (IM4). (13) farm24.Rdata: Parameters and data for the site in the Broughton Archipegalo (BCB). (14) farmWCVI.Rdata: … for a site on the west coast of Vancouver Island (BCV). (15) farmCC.Rdata: … for a site on the central coast of BC (BCC). (16) farmNB.Rdata: … for a site in New Brunswick (NB). (17) farmNS.Rdata: … for a site in Nova Scotia (NS). (18) farmNL.Rdata: ... data is from Newfoundland (NL). (19) farmNLI.Rdata: … for the Lista site in Norway (NLI). (20) farmNIN.Rdata: … for the Ingoy site in Norway (NIN). (21) ParamsFuncs.Rdata: Save parameterized functions (see Figure S1) (22) Summary.Rdata: produced by Figure2_R0Calcs.R and loaded by Figure2_R0Graphs.R
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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 | 0.001 | 0.002 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.000 | 0.001 |
| Research integrity | 0.000 | 0.001 |
| Insufficient payload (model declined to judge) | 0.046 | 0.006 |
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".