Doptim                  D-family optimization function
Dtrace                  Trace optimization routines
LEDoptim                Optimization function for D-family, E-family
                        and Laplace approximated ED designs
LinMatrixH              Model linearization with respect to epsilon.
LinMatrixL              The linearized matrix L
LinMatrixLH             Model linearization with respect to epsilon and
                        eta.
LinMatrixL_occ          Model linearization with respect to occasion
                        variablity parameters.
PopED-package           PopED - *Pop*ulation (and individual) optimal
                        *E*xperimental *D*esign.
RS_opt                  Optimize the objective function using an
                        adaptive random search algorithm for D-family
                        designs.
RS_opt_gen              Optimize the objective function using an
                        adaptive random search algorithm for D-family
                        and E-family designs.
a_line_search           Optimize using line search
bfgsb_min               Nonlinear minimization using BFGS with box
                        constraints
blockexp                Summarize your experiment for optimization
                        routines
blockfinal              Result function for optimization routines
blockheader             Header function for optimization routines
blockopt                Summarize your optimization settings for
                        optimization routines
calc_autofocus          Compute the autofocus portion of the stochastic
                        gradient routine
calc_ofv_and_fim        Calculate the Fisher Information Matrix (FIM)
                        and the OFV(FIM) for either point values or
                        parameters or distributions.
calc_ofv_and_grad       Compute an objective function and gradient
cell                    MATLAB cell function
convert_variables       Create global variables in the PopED database
create.poped.database   Create a PopED database
create_design           Create design variables for a full description
                        of a design.
create_design_space     Create design variables and a design space for
                        a full decription of an optimization problem.
diag_matlab             Function written to match MATLAB's diag
                        function
downsizing_general_design
                        Downsize a general design to a specific design
ed_laplace_ofv          Evaluate the expectation of determinant the
                        Fisher Information Matrix (FIM) using the
                        Laplace approximation.
ed_mftot                Evaluate the expectation of the Fisher
                        Information Matrix (FIM) and the expectation of
                        the OFV(FIM).
evaluate.e.ofv.fim      Evaluate the expectation of the Fisher
                        Information Matrix (FIM) and the expectation of
                        the OFV(FIM).
evaluate.fim            Evaluate the Fisher Information Matrix (FIM)
feps.add                RUV model: Additive .
feps.add.prop           RUV model: Additive and Proportional.
feps.prop               RUV model: Proportional.
feval                   MATLAB feval function
ff.PK.1.comp.oral.md.CL
                        Structural model: one-compartment, oral
                        absorption, multiple bolus dose, parameterized
                        using CL.
ff.PK.1.comp.oral.md.KE
                        Structural model: one-compartment, oral
                        absorption, multiple bolus dose, parameterized
                        using KE.
ff.PK.1.comp.oral.sd.CL
                        Structural model: one-compartment, oral
                        absorption, single bolus dose, parameterized
                        using CL.
ff.PK.1.comp.oral.sd.KE
                        Structural model: one-compartment, oral
                        absorption, single bolus dose, parameterized
                        using KE.
ff.PKPD.1.comp.oral.md.CL.imax
                        Structural model: one-compartment, oral
                        absoprtion, multiple bolus dose, parameterized
                        using CL driving an inhibitory IMAX model with
                        a direct efect.
ff.PKPD.1.comp.sd.CL.emax
                        Structural model: one-compartment, single bolus
                        IV dose, parameterized using CL driving an EMAX
                        model with a direct efect.
fileparts               MATLAB fileparts function
getTruncatedNormal      Generate a random sample from a truncated
                        normal distribution.
get_all_params          Extract all model parameters from the PopED
                        database.
get_rse                 Compute the expected parameter relative
                        standard errors
getfulld                Create a full D (between subject variability)
                        matrix given a vector of variances and
                        covariances.
gradf_eps               Model linearization with respect to epsilon.
isempty                 Function written to match MATLAB's isempty
                        function
isfield                 Function written to match MATLAB's isfield
                        function
log_prior_pdf           Compute the natural log of the PDF for the
                        parameters in an E-family design
mf                      The full Fisher Information Matrix (FIM) for
                        one individual
mf3                     The reduced Fisher Information Matrix (FIM) for
                        one individual
mf5                     The reduced Fisher Information Matrix (FIM) for
                        one individual, using the SD of RUV as a
                        parameter.
mf6                     The full Fisher Information Matrix (FIM) for
                        one individual parameterized with A,B,C
                        matrices & using the derivative of variance.
mf7                     The full Fisher Information Matrix (FIM) for
                        one individual Calculating one model switch at
                        a time, good for large matrices.
mf8                     The reduced Fisher Information Matrix (FIM) for
                        one individual parameterized with A,B,C
                        matrices & using the derivative of variance.
mfea                    Modified Federov Exchange Algorithm
mftot                   Evaluate the Fisher Information Matrix (FIM)
mftot0                  The full Fisher Information Matrix (FIM)
mftot1                  The reduced Fisher Information Matrix (FIM)
mftot2                  The Fisher Information Matrix (FIM) using
                        weighted models
mftot3                  The Fisher Information Matrix (FIM) some other
                        method
mftot4                  The reduced Fisher Information Matrix (FIM)
                        using the SD of RUV as a parameter.
mftot5                  The full Fisher Information Matrix (FIM)
                        parameterized with A,B,C matrices & using the
                        derivative of variance.
mftot6                  The full Fisher Information Matrix (FIM)
                        Calculating one model switch at a time, good
                        for large matrices.
mftot7                  The reduced Fisher Information Matrix (FIM)
                        parameterized with A,B,C matrices & using the
                        derivative of variance.
model_prediction        Model predictions
ofv_criterion           Normalize an objective function by the size of
                        the FIM matrix
ofv_fim                 Evaluate a criterion of the Fisher Information
                        Matrix (FIM)
ones                    Creates a matrix of ones
pargen                  Parameter simulation
plot_efficiency_of_windows
                        Plot the efficiency of windows
plot_model_prediction   Plot model predictions
poped.choose            Choose between 'arg1' and 'arg2'
poped_optimize          Optimization main module for PopED
rand                    Function written to match MATLAB's rand
                        function
randn                   Function written to match MATLAB's randn
                        function
randperm                Function written to match MATLAB's randperm
                        function
size                    Function written to match MATLAB's size
                        function
test_for_max            Test if any matrix element is above a max
                        value.
test_for_min            Test if any matrix element is above a minimum
                        value.
test_for_zeros          Test if any matrix element is zero.
test_mat_size           Test to make sure that matricies are the right
                        size
tic                     Timer function (as in MATLAB)
toc                     Timer function (as in MATLAB)
zeros                   Creates a matrix of zeros.
