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Changelog

Source: NEWS.md

fb4package 2.1.0 (2026-06-06)

CRAN release: 2026-06-09

New features

  • Nutrient sub-model now active — Bioenergetic() accepts nutrient_data (N and P concentrations, assimilation efficiencies). When supplied, run_fb4() computes daily nitrogen and phosphorus fluxes (consumed, growth, excretion, egestion, N:P ratios) and appends them to daily_output.

  • Contaminant sub-model now active — Bioenergetic() accepts contaminant_data. All three CONTEQ equations (pure accumulation, T/W-dependent elimination, Arnot & Gobas 2004) are now computed within the daily loop and returned as Contaminant_* columns in daily_output.

  • Expanded daily_output — three columns added: Starting_Weight (body weight at the start of each day), Mean_Prey_Energy_J_g (energy-weighted mean prey energy density), and per-prey consumption columns (Cons_<prey>_g) for each diet item.

  • Validation vignette — new article “Validation against FB4-Shiny” (vignettes/fb4-shiny-validation.Rmd) verifies numerical equivalence with FB4-Shiny v1.1.7 across all five simulation modes and the nutrient and contaminant sub-models.

Bug fixes

  • strategy = "direct" now correctly infers the concrete sub-strategy from fit_to: "Ration_prey" routes to direct_ration_grams and "Ration" routes to direct_ration_percent, instead of always defaulting to direct_p_value (#strategy-interface).

  • TMB C++ engine (src/fb4_main.cpp): total consumption, respiration, and waste fluxes are now accumulated using start-of-day weight, consistent with the R simulation engine.

  • extract_hierarchical_parameters(): betas_se is no longer overwritten if already populated; uses NA_real_ instead of bare NA.

fb4package 2.0.0 (2026-03-28)

CRAN release: 2026-05-07

This is a major rewrite. The entire codebase was reorganised from a monolithic structure (7 files) into a modular, strategy-based architecture (33 files), and an optional TMB/C++ backend was added for statistical estimation methods.

New features

TMB backend
  • Added optional TMB (Template Model Builder) backend for maximum likelihood and hierarchical estimation, providing 10–50× speedup over the pure-R implementation (src/fb4_main.cpp).
  • New C++ headers for consumption, respiration, egestion/excretion, body composition, and validation (src/includes/).
  • Added Rcpp, TMB (>= 1.7.0), RcppEigen as dependencies. R (>= 4.0.0) is now required (was >= 3.5.0).
New estimation strategies via run_fb4(strategy = ...)
  • "optim" — gradient-based fitting with stats::optim().
  • "mle" — maximum likelihood estimation of p-value with SE and 95% CI, using observed final weights (observed_weights).
  • "bootstrap" — non-parametric uncertainty quantification via resampling of observed final weights. Supports parallel execution (future/furrr).
  • "hierarchical" — population-level mixed-effects model estimating mean and SD of p across individuals (TMB required).
Architecture
  • Simulation engine extracted into R/12-simulation-engine.R.
  • Fitting algorithms split into individual strategy files (14.2.1 through 14.2.6), a shared commons layer (14.0.1-strategy-commons.R), and a strategy interface (14.1).
  • Validation split into four specialised modules (11.0-core, 11.1-basic, 11.2-parameter, 11.3-data, 11.4-main).
  • Bioenergetic class and methods separated into 13.0-bioenergetic-classes.R and 13.1-bioenergetic-methods.R.
  • Analysis layer split into five focused modules (15.0–15.4).
  • Plot layer split into four modules (16.1–16.4) covering core helpers, daily output plots, analysis plots, and bioenergetic-object plots.
  • Result builders centralised in 14.3-result-builders.R with consistent field names (p_value, total_consumption_g, converged) across all strategies.
New analysis functions

analyze_growth_patterns(), analyze_feeding_performance(), analyze_energy_budget(), analyze_growth_temperature_sensitivity(), analyze_population_variation(), comprehensive_nutritional_analysis().

New plot types

plot.fb4_result(type = "growth" | "consumption" | "temperature" | "energy" | "uncertainty" | "dashboard") and plot.Bioenergetic(type = "temperature" | "diet" | "energy_density" | "sensitivity").

Internal changes

  • R/00-utils.R (v0.1.0) replaced by R/utils.R with additional helpers (z_score(), safe_exp(), safe_sqrt(), clamp(), %||%).
  • R/09-fitting-algorithms.R replaced by the strategy layer (14.x).
  • R/10-main-growth-model.R and R/12-fb4-main.R replaced by R/12-simulation-engine.R and R/14.0-run-fb4-orchestrator.R.
  • R/13-visualization-analysis.R split into 15.x (analysis) and 16.x (plots).
  • R/14-bioenergetic-classes.R split into 13.0 and 13.1.

fb4package 0.1.0

  • Initial release. Pure-R implementation of Fish Bioenergetics 4.0 (Deslauriers et al. 2017).
  • Binary search fitting (strategy = "binary_search") and direct p-value simulation (strategy = "direct").
  • Bioenergetic S3 class with print(), summary(), plot(), and run_fb4() methods.
  • Species parameter database for 105 models (73 species).
  • No compiled code; depends only on base R packages.