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      "page": "mp_linear",
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        "Alternative Classes",
        "Argument Fields",
        "Static Fields",
        "Standard Methods",
        "Composition",
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        "Method Caching"
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      "filename": "elementwise_binary_operators.html",
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      "headings": [
        "The Problem",
        "Definition of an Elementwise Binary Operator in the C++ Engine",
        "Forcing a Binary Operator in R to have these Properties",
        "Step 1",
        "Step 2",
        "Step 3",
        "Implementation and Examples"
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      "filename": "engine_agnostic_grammar.html",
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        "Amuse bouche: a structured SIR model",
        "Appetizer: specifying the basic SIR model",
        "Main course: expanding the basic SIR with additional structure",
        "Dessert: understanding model simulation in macpan2"
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        "Using Examples",
        "Modifying Examples"
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        "Setup and Example Models and Data",
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        "What does macpan2 mean?",
        "Why do most of the functions start with mp_?",
        "Why do some of the functions start with mp_tmb_?",
        "Calibration Details and Outputs",
        "How does macpan2 fit models to data?",
        "How does macpan2 derive confidence intervals?",
        "What likelihood and prior distribution assumptions does macpan2 make?",
        "Can I get a new model specification with fitted parameters as defaults, from a calibrated calibrator object?",
        "Plotting Simulated Trajectories",
        "How can I plot simulated trajectories?",
        "How can I plot a calibrated model with the observed data used in the calibration?",
        "Calibration Troubleshooting",
        "Should I worry about NA/NaN function evaluation warnings?",
        "What should I do if I do not converge?",
        "How do I increase the number of iterations that the optimizer takes?",
        "Parameter Estimation and Uncertainty",
        "What can I do when my confidence intervals include zero for a parameter that should be positive?",
        "Can I weight the importance of trajectories when fitting to more than one of them?",
        "Dynamical Instabilities",
        "What is the best way for me to keep my state variables from going negative?",
        "Initial Conditions",
        "My data start mid-epidemic: how do I know what the initial number of infectious individuals is?",
        "Coding Style",
        "What does |> mean?",
        "Why do you put weird symbols at the start of lines?",
        "Time Variation of Parameters",
        "How can I use a known time series of values?",
        "What if my time-series has missing values?",
        "What can I do if I do not know the functional form of time-variation?",
        "Under Reporting, Delayed Reporting, and Total Reporting",
        "How should I account for under-reporting in macpan2?",
        "How should I account for delayed reporting as well as under-reporting in macpan2?",
        "Can macpan2 use hidden Markov models to account for reporting bias?",
        "Stochastic Simulation",
        "How can I set the seed for the random number generator?",
        "Why do I keep getting the same result even though my model has randomness?",
        "What are the mathematical details of the Euler multinomial process error model?",
        "Does macpan2 implement the Gillespie algorithm?",
        "More Process Error (incomplete)"
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        "SIR Model",
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        "Set up the Optimizer",
        "Run the Optimization",
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        "Hazard",
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        "Absolute Flows",
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        "Expressions",
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        "Assignment Parse Tables",
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      "modified": "2025-04-22 01:03:42",
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