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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.
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.
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.
src/fb4_main.cpp).src/includes/).Rcpp, TMB (>= 1.7.0),
RcppEigen as dependencies. R (>= 4.0.0) is
now required (was >= 3.5.0).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).R/12-simulation-engine.R.14.2.1 through 14.2.6), a shared commons
layer (14.0.1-strategy-commons.R), and a strategy interface
(14.1).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.15.0–15.4).16.1–16.4) covering core helpers, daily
output plots, analysis plots, and bioenergetic-object plots.14.3-result-builders.R
with consistent field names (p_value,
total_consumption_g, converged) across all
strategies.analyze_growth_patterns(),
analyze_feeding_performance(),
analyze_energy_budget(),
analyze_growth_temperature_sensitivity(),
analyze_population_variation(),
comprehensive_nutritional_analysis().
plot.fb4_result(type = "growth" | "consumption" | "temperature" | "energy" | "uncertainty" | "dashboard")
and
plot.Bioenergetic(type = "temperature" | "diet" | "energy_density" | "sensitivity").
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.strategy = "binary_search") and
direct p-value simulation
(strategy = "direct").Bioenergetic S3 class with print(),
summary(), plot(), and run_fb4()
methods.These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.