Population (and Individual) Optimal Experimental Design

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Documentation for package ‘PopED’ version 0.2.0

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PopED-package PopED - *Pop*ulation (and individual) optimal *E*xperimental *D*esign.
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
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 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
getfulld Create a full D (between subject variability) matrix given a vector of variances and covariances.
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
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
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.
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 PopED - *Pop*ulation (and individual) optimal *E*xperimental *D*esign.
poped PopED - *Pop*ulation (and individual) optimal *E*xperimental *D*esign.
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
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.
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.