| 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... |
| build_sfg | Build PopED parameter function from a model function |
| calc_autofocus | Compute the autofocus portion of the stochastic gradient... |
| calc_ofv_and_fim | Calculate the Fisher Information Matrix (FIM) and the... |
| calc_ofv_and_grad | Compute an objective function and gradient |
| cell | Create a cell array (a matrix of lists) |
| convert_variables | Create global variables in the 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... |
| create.poped.database | Create a PopED database |
| design_summary | Display a summary of output from poped_db |
| diag_matlab | Function written to match MATLAB's diag function |
| Doptim | D-family optimization function |
| downsizing_general_design | Downsize a general design to a specific design |
| Dtrace | Trace optimization routines |
| ed_laplace_ofv | Evaluate the expectation of determinant the Fisher... |
| ed_mftot | Evaluate the expectation of the Fisher Information Matrix... |
| efficiency | Compute efficiency. |
| evaluate_design | Evaluate a design |
| evaluate.e.ofv.fim | Evaluate the expectation of the Fisher Information Matrix... |
| evaluate.fim | Evaluate the Fisher Information Matrix (FIM) |
| evaluate_fim_map | Compute the Bayesian Fisher information matrix |
| evaluate_power | Power of a design to estimate a parameter. |
| extract_norm_group_fim | Extract a normalized group 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... |
| ff.PK.1.comp.oral.md.KE | Structural model: one-compartment, oral absorption, multiple... |
| ff.PK.1.comp.oral.sd.CL | Structural model: one-compartment, oral absorption, single... |
| ff.PK.1.comp.oral.sd.KE | Structural model: one-compartment, oral absorption, single... |
| ff.PKPD.1.comp.oral.md.CL.imax | Structural model: one-compartment, oral absorption, multiple... |
| ff.PKPD.1.comp.sd.CL.emax | Structural model: one-compartment, single bolus IV dose,... |
| fileparts | MATLAB fileparts function |
| get_all_params | Extract all model parameters from the PopED database. |
| getfulld | Create a full D (between subject variability) matrix given a... |
| get_rse | Compute the expected parameter relative standard errors |
| getTruncatedNormal | Generate a random sample from a truncated normal... |
| get_unfixed_params | Return all the unfixed parameters |
| gradf_eps | Model linearization with respect to epsilon. |
| inv | Compute the inverse of a matrix |
| isempty | Function written to match MATLAB's isempty function |
| LEDoptim | Optimization function for D-family, E-family and Laplace... |
| 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 variability... |
| log_prior_pdf | Compute the natural log of the PDF for the parameters in an... |
| mc_mean | Compute the monte-carlo mean of a function |
| median_hilow_poped | Wrap summary functions from Hmisc and ggplot to work with... |
| mf3 | The Fisher Information Matrix (FIM) for one individual |
| mf7 | The full Fisher Information Matrix (FIM) for one individual... |
| mfea | Modified Fedorov Exchange Algorithm |
| mftot | Evaluate the Fisher Information Matrix (FIM) |
| 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 | Create a matrix of ones |
| optim_ARS | Optimize a function using adaptive random search. |
| optimize_groupsize | Title Optimize the proportion of individuals in the design... |
| optimize_n_eff | Translate efficiency to number of subjects |
| optimize_n_rse | Optimize the number of subjects based on desired uncertainty... |
| optim_LS | Optimize a function using a line search algorithm. |
| pargen | Parameter simulation |
| plot_efficiency_of_windows | Plot the efficiency of windows |
| plot_model_prediction | Plot model predictions |
| PopED | PopED - *Pop*ulation (and individual) optimal *E*xperimental... |
| poped.choose | Choose between 'arg1' and 'arg2' |
| poped_gui | Run the graphical interface for PopED |
| poped_optim | Optimize a design defined in a PopED database |
| poped_optim_1 | Optimization main module for PopED Optimize the objective... |
| poped_optim_2 | Optimization main module for PopED |
| poped_optim_3 | Optimization main module for PopED |
| poped_optimize | Retired optimization module for PopED |
| rand | Function written to match MATLAB's rand function |
| randn | Function written to match MATLAB's randn function |
| RS_opt | Optimize the objective function using an adaptive random... |
| shrinkage | Predict shrinkage of empirical Bayes estimates (EBEs) in a... |
| size | Function written to match MATLAB's size function |
| start_parallel | Start parallel computational processes |
| summary.poped_optim | Display a summary of output from poped_optim |
| 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) |
| tryCatch.W.E | tryCatch both warnings (with value) and errors |
| zeros | Create a matrix of zeros. |
