Changes in version 2.0.0 (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.

                        Changes in version 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.