Add new food-habits data pipeline in data-raw/food-habits (ingestion, estimators, exports)

[david-beauchesne]

Summary

This PR introduces a new implementation for food-habits data products in data-raw/food-habits/.

The implementation is intentionally isolated to data-raw/food-habits/ and does not modify existing package runtime code.

What was implemented

1) Processing workflow

Updated data-raw/food-habits/food-habits.R as the orchestration script.
It handles input loading, standardization, filtering/grouping configuration, estimation workflows, and export/save of outputs.

2) Utilities and shared helpers

Added data-raw/food-habits/food-habits-utils.R with:

• input-path resolution and loading helpers
• data standardization and joins (predator/prey code/name mapping)
• filtering and optional code-grouping logic
• plot export utilities

3) Mean-diet estimator

Added data-raw/food-habits/food-habits-estimate-mean-diet.R with:

• stratified estimator using predator-length and survey-stratum aggregation
• optional label-column enrichment
• optional prey exclusion list
• optional custom length/strata weights
• configurable denominator mode for predator counts

4) Dominant prey summaries

Added data-raw/food-habits/food-habits-estimate-dominant-prey.R:

• built from estimate_mean_diet()
• supports top-N and threshold filters

5) Predator contribution summaries

Added data-raw/food-habits/food-habits-estimate-predator-contribution.R:

• summarizes predator contribution to focal prey
• supports top-N predator filtering and contribution thresholds

Outputs produced by workflow

The pipeline produces:

• food_habits_full
• food_habits_stomach
• food_habits_species
• food_habits_mean_diet_stratified
• food_habits_dominant_prey_timeseries
• food_habits_prey_predation

Outputs are saved in data-raw/food-habits/*.rda and exported with usethis::use_data(...).

Examples and figures

If run_examples <- TRUE in the processing script, figures are automatically exported.

[EOGrady21]

@david-beauchesne
This pull request cannot be merged due to unresolved conflicts. I do not have permission to write to the head branch

Conflicts should be resolved on inSileco:main, I don't anticipate they are anything major but I Cannot see the details unfortunately

[KevCaz]

@EOGrady21 conflicts should be resolved now. Let me know if you need something else.