Index
  • ad_comm::change_datafile_name
  • ad_comm::change_pinfile_name
  • arrmblsize
  • convergence_criteria
  • funnel_dvariable use with ad_begin_funnel
  • STD
  • !! LOCAL_CALCS
  • 3darray
  • 4darray
  • 5darray
  • 6darray
  • 7darray
  • Accessing elements of matrix objects
  • active parameters
  • active() function
  • 2
  • adjoint code
  • ad_begin_funnel reducing the amount of temporary storage
  • arrays
    3darray
  • 4darray
  • 5darray
  • 6darray
  • 7darray
  • four dimensional
  • four dimensional
  • matrix
  • three dimensional
  • three dimensional
  • vector
  • arrmblsize
  • Automatic differentiation
  • Bayesian inference profile likelihood
  • BETWEEN_PHASES_SECTION
  • binary files
    how to read them
  • uistream
  • uostream
  • chemical engineering
  • chemical kinetics
  • column
    extract a column from a matrix
  • 2
  • command line arguments
    -ind NAME input data file
  • -lprof profile likelihood
  • -mcdiag
  • -mceval
  • -mcmc N Markov chain Monte Carlo
  • -mcmult
  • -mcr
  • -mcsave
  • -mcscale
  • comments in data file
  • confidence limits
    use of profile likelihood
  • 2
  • 3
  • convergence criterion
  • correlation matrix
  • current_phase() function
  • 2
  • 3
  • data file
  • default behaviour
  • default file names
  • default number of function evaluations
  • difference equation
    explicit form
  • numerical stability
  • semi-implicit form
  • differential equations implicit methods
  • element-wise operations
  • endl stream manipulator
  • examples short description of
  • Financial modelling
  • Fisheries catch-at-age model
  • fisheries management
  • fitting_criterion
  • five dimensional arrays
  • four dimensional arrays
  • 2
  • 3
  • FUNCTION keyword
  • function minimizer
    default behaviour
  • modifying default behaviour
  • FUNCTION
  • 2
  • GARCH Model
  • GLOBALS_SECTION
  • gradient_structure::set_ARRAY_MEMBLOCK_SIZE
    the correct way to set
  • 2
  • gradient_structure::set_CMPDIF_BUFFER_SIZE
  • gradient_structure::set_GRADSTACK_BUFFER_SIZE
  • 2
  • gradient_structure::set_MAX_NUM_DEPENDENT_VARIABLES
  • gradient_structure::set_MAX_NVAR_OFFSET
  • Hastings-Metropolis algorithm
  • INITIALIZATION_SECTION
  • init_bounded_dev_vector
  • init_bounded_number
  • 2
  • 3
  • init_bounded_vector
  • input changing the default file names
  • last_phase() function
  • least squares
  • likeprof_number
  • LOCAL_CALCS
    !!
  • use instead of the PRELIMINARY_CALCS_SECTION
  • 3
  • Markov chain simulation
    Hastings-Metropolis algorithm
  • to estimate the posterior distribution
  • matrix objects accessing elements of
  • mceval_phase()
  • minimization
    phases
  • phases
  • multi-phase minimization
  • 2
  • 3
  • 4
  • nonlinear regression
  • numerical integration
  • objective_function_value
  • operator ++ used to increment the valid index bounds
  • operator -- used to decrement the valid index bounds
  • optimization
    phases
  • phases
  • optional extras
  • output files
  • PARAMETER_SECTION
  • PRELIMINARY_CALCS_SECTION
  • 2
  • PROCEDURE_SECTION
  • profile likelihood
    confidence limits
  • 2
  • putting bounds on initial parameters
  • 2
  • regression
    nonlinear
  • robust
  • REPORT_SECTION
    example of
  • example of
  • robust regression
  • 2
  • RUNTIME_SECTION
  • Schaeffer -- Pella-Tomlinson model
    Bayesian considerations
  • optimal productivity
  • unfished equilibrium biomass level
  • 4
  • sdreport_matrix
  • 2
  • sdreport_number
  • 2
  • sdreport_vector
  • 2
  • sd_phase() function
  • SECTIONS
    DATA_SECTION
  • GLOBALS_SECTION
  • PARAMETER_SECTION
  • PARAMETER_SECTION
  • PRELIMINARY_CALCS_SECTION
  • PROCEDURE_SECTION
  • REPORT_SECTION
  • RUNTIME_SECTION
  • BETWEEN_PHASES_SECTION
  • PRELIMINARY_CALCS_SECTION
  • set_stepnumber
  • set_stepsize
  • seven dimensional arrays
  • simple example
  • six dimensional arrays
  • 2
  • standard deviation report
  • standard deviations report
    STD
  • 2
  • SUBROUTINE
  • subvector operation
    avoiding loops with
  • examples of
  • syntax rules
  • template sections
  • template
  • 2
  • The GLOBALS_SECTION
  • three dimensional arrays
  • 2
  • 3
  • 4
  • time series GARCH Model
  • TOP_OF_MAIN section
  • 2
  • use of regression function
  • use of vector and matrix calculations
  • vector operations