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Type 'q()' to quit R. > # This file is part of the standard testthat infrastructure. > # Run all tests with: devtools::test() or testthat::test_local() > > library(testthat) > library(fb4package) > > test_check("fb4package") Bioenergetic object created for: Oncorhynchus tshawytscha Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. FB4 Simulation Results ========================= Species: Oncorhynchus tshawytscha Method: Direct Execution Duration: 30 days RESULTS: Initial weight: 800 g Final weight: 848.18 g Growth: 6% Total consumption: 267.11 g P_value: 0.5 FITTING: [OK] Successful Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. FB4 Simulation Results ========================= Species: Oncorhynchus tshawytscha Method: Direct Execution Duration: 30 days RESULTS: Initial weight: 800 g Final weight: 848.18 g Growth: 6% Total consumption: 267.11 g P_value: 0.5 FITTING: [OK] Successful ---------------------------------------- DETAILED INFORMATION ---------------------------------------- EXECUTION: Backend: r Version: 2.0.0 Execution time: 0.01 seconds Timestamp: 2026-04-11 07:08:17 OUTPUT DATA: Daily values: 30 days Variables: Weight, Temperature Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. FB4 Simulation Results ========================= Species: Oncorhynchus tshawytscha Method: Maximum Likelihood Duration: 30 days MAXIMUM LIKELIHOOD ESTIMATION: Observations: 15 weights Initial weight: 800 g Predicted weight: 899.85 g PARAMETER ESTIMATES: P_value: 0.8033 ± NA 95% CI: [NA, NA] Measurement error (sigma): 0.014 MODEL FIT: Log-likelihood: -58.76 AIC: 121.53 Converged: [OK] Yes Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Validation warnings: Missing optional parameters (will be calculated): CX Object is ready for simulation Processing species parameters... Processing temporal data... Processing simulation settings... Simulation data preparation complete. Ready for simulation. FB4 Bioenergetic Model ========================= Species: Oncorhynchus tshawytscha (Chinook salmon) Setup: 800 g -> 30 days Components: [OK] Parameters: 38 params (consumption, respiration, activity, sda, egestion, excretion, predator) [OK] Temperature: 30 days (4.5-6.3°C) [OK] Diet: 2 prey species, 30 days Status: Ready for fitting FB4 Bioenergetic Model - Detailed Summary ============================================= SPECIES: Scientific: Oncorhynchus tshawytscha Common: Chinook salmon Life stage: adult PARAMETERS: Consumption (9): CA = 0.303 CB = -0.275 CQ = 3 CTO = 15 CTM = 20 ... (4 more) Respiration (10): RA = 0.00264 RB = -0.217 RQ = 0.06818 RTO = 0.0234 RTM = 0 ... (5 more) Activity (2): ACT = 1 BACT = 0 Sda (1): SDA = 0.172 Egestion (4): FA = 0.212 FB = -0.222 FG = 0.631 ... (1 more) Excretion (4): UA = 0.0314 UB = 0.58 UG = -0.299 ... (1 more) Predator (8): PREDEDEQ = 2 Alpha1 = 4500 Beta1 = 6 ... (5 more) ENVIRONMENT: Temperature: 5.3°C (mean) Range: 4.5 - 6.3°C Duration: 30 days (1 to 30) DIET: Prey species: 2 Coverage: 30 days Main prey: 1. Alewife: 70% 2. Shrimp: 30% Energy density: 3200 - 4900 J/g SIMULATION: Initial Weight: 800 g Duration: 30 days STATUS: Ready: 4 /4 components - Ready for fitting! [ FAIL 0 | WARN 61 | SKIP 1 | PASS 172 ] ══ Skipped tests (1) ═══════════════════════════════════════════════════════════ • SE not available (optimization did not converge) (1): 'test-14b-strategies-mle-hierarchical.R:159:5' [ FAIL 0 | WARN 61 | SKIP 1 | PASS 172 ] > > proc.time() user system elapsed 30.06 0.40 30.46