PopED: Population (and Individual) Optimal Experimental Design

Optimal experimental designs for both population and individual studies based on nonlinear mixed-effect models. Often this is based on a computation of the Fisher Information Matrix. This package was developed for pharmacometric problems, and examples and predefined models are available for these types of systems.

AuthorAndrew C. Hooker [aut, cre, trl, cph], Sebastian Ueckert [aut] (MATLAB version), Marco Foracchia [aut] (O-Matrix version), Joakim Nyberg [aut] (MATLAB version), Eric Stroemberg [ctb] (MATLAB version)
Date of publication2016-12-12 18:16:19
MaintainerAndrew C. Hooker <andrew.hooker@farmbio.uu.se>
LicenseLGPL (>= 3)
Version0.3.2
http://poped.sourceforge.net

View on CRAN

Man pages

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...

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

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)

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 absoprtion, 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

isfield: Function written to match MATLAB's isfield 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 variablity...

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...

mf: The full Fisher Information Matrix (FIM) for one individual

mf3: The reduced Fisher Information Matrix (FIM) for one...

mf5: The reduced Fisher Information Matrix (FIM) for one...

mf6: The full Fisher Information Matrix (FIM) for one individual...

mf7: The full Fisher Information Matrix (FIM) for one individual...

mf8: The reduced Fisher Information Matrix (FIM) for one...

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...

mftot5: The full Fisher Information Matrix (FIM) parameterized with...

mftot6: The full Fisher Information Matrix (FIM) Calculating one...

mftot7: The reduced Fisher Information Matrix (FIM) parameterized...

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

optim_ARS: Optimization Using Adaptive Random Search.

optim_LS: Optimization 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: Optimization main module for PopED

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...

RS_opt_gen: Optimize the objective function using an adaptive random...

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_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.

Functions

a_line_search Man page
bfgsb_min Man page
blockexp Man page
blockfinal Man page
blockheader Man page
blockopt Man page
calc_autofocus Man page
calc_ofv_and_fim Man page
calc_ofv_and_grad Man page
cell Man page
convert_variables Man page
create_design Man page
create_design_space Man page
create.poped.database Man page
diag_matlab Man page
Doptim Man page
downsizing_general_design Man page
Dtrace Man page
ed_laplace_ofv Man page
ed_mftot Man page
efficiency Man page
evaluate_design Man page
evaluate.e.ofv.fim Man page
evaluate.fim Man page
feps.add Man page
feps.add.prop Man page
feps.prop Man page
feval Man page
ff.PK.1.comp.oral.md.CL Man page
ff.PK.1.comp.oral.md.KE Man page
ff.PK.1.comp.oral.sd.CL Man page
ff.PK.1.comp.oral.sd.KE Man page
ff.PKPD.1.comp.oral.md.CL.imax Man page
ff.PKPD.1.comp.sd.CL.emax Man page
fileparts Man page
get_all_params Man page
getfulld Man page
get_rse Man page
getTruncatedNormal Man page
get_unfixed_params Man page
gradf_eps Man page
inv Man page
isempty Man page
isfield Man page
LEDoptim Man page
LinMatrixH Man page
LinMatrixL Man page
LinMatrixLH Man page
LinMatrixL_occ Man page
log_prior_pdf Man page
mc_mean Man page
median_hilow_poped Man page
mf Man page
mf3 Man page
mf5 Man page
mf6 Man page
mf7 Man page
mf8 Man page
mfea Man page
mftot Man page
mftot0 Man page
mftot1 Man page
mftot2 Man page
mftot3 Man page
mftot4 Man page
mftot5 Man page
mftot6 Man page
mftot7 Man page
model_prediction Man page
ofv_criterion Man page
ofv_fim Man page
ones Man page
optim_ARS Man page
optim_LS Man page
pargen Man page
plot_efficiency_of_windows Man page
plot_model_prediction Man page
poped Man page
PopED Man page
poped.choose Man page
poped_gui Man page
poped_optim Man page
poped_optimize Man page
PopED-package Man page
rand Man page
randn Man page
randperm Man page
RS_opt Man page
RS_opt_gen Man page
size Man page
start_parallel Man page
summary.poped_optim Man page
test_for_max Man page
test_for_min Man page
test_for_zeros Man page
test_mat_size Man page
tic Man page
toc Man page
zeros Man page

Files

PopED
PopED/inst
PopED/inst/examples
PopED/inst/examples/ex.1.b.PK.1.comp.oral.md.re-parameterize.R
PopED/inst/examples/two_comp_oral_CL.c
PopED/inst/examples/ex.9.PK.2.comp.oral.md.ode.compiled.R
PopED/inst/examples/ex.10.PKPD.HCV.compiled.R
PopED/inst/examples/ex.7.PK.1.comp.maturation.R
PopED/inst/examples/ex.1.c.PK.1.comp.oral.md.ODE.compiled.R
PopED/inst/examples/ex.1.a.PK.1.comp.oral.md.intro.R
PopED/inst/examples/ex.8.tmdd_qss_one_target_compiled.R
PopED/inst/examples/ex.2.a.warfarin.evaluate.R
PopED/inst/examples/ex.3.b.PKPD.1.comp.oral.md.imax.ED-opt.R
PopED/inst/examples/ex.4.PKPD.1.comp.emax.R
PopED/inst/examples/ex.2.e.warfarin.Ds.R
PopED/inst/examples/ex.2.b.warfarin.optimize.R
PopED/inst/examples/ex.6.PK.1.comp.oral.sd.R
PopED/inst/examples/ex.2.c.warfarin.ODE.compiled.R
PopED/inst/examples/ex.5.PD.emax.hill.R
PopED/inst/examples/ex.2.d.warfarin.ED.R
PopED/inst/examples/tmdd_qss_one_target.c
PopED/inst/examples/one_comp_oral_CL.c
PopED/inst/examples/HCV_ode.c
PopED/inst/examples/ex.3.a.PKPD.1.comp.oral.md.imax.D-opt.R
PopED/inst/CITATION
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PopED/NAMESPACE
PopED/NEWS
PopED/R
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PopED/vignettes/intro-poped_files/figure-html/simulate_with_BSV-1.png
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PopED/README.md
PopED/MD5
PopED/build
PopED/build/vignette.rds
PopED/DESCRIPTION
PopED/man
PopED/man/Dtrace.Rd PopED/man/isempty.Rd PopED/man/calc_ofv_and_fim.Rd PopED/man/create_design.Rd PopED/man/mftot3.Rd PopED/man/mftot5.Rd PopED/man/mf8.Rd PopED/man/downsizing_general_design.Rd PopED/man/mftot2.Rd PopED/man/calc_autofocus.Rd PopED/man/create_design_space.Rd PopED/man/calc_ofv_and_grad.Rd PopED/man/LinMatrixH.Rd PopED/man/ff.PK.1.comp.oral.md.KE.Rd PopED/man/LinMatrixLH.Rd PopED/man/test_for_max.Rd PopED/man/toc.Rd PopED/man/poped_gui.Rd PopED/man/mftot.Rd PopED/man/mftot1.Rd PopED/man/ff.PKPD.1.comp.sd.CL.emax.Rd PopED/man/convert_variables.Rd PopED/man/ones.Rd PopED/man/mf.Rd PopED/man/test_for_zeros.Rd PopED/man/plot_model_prediction.Rd PopED/man/fileparts.Rd PopED/man/zeros.Rd PopED/man/optim_LS.Rd PopED/man/rand.Rd PopED/man/mftot0.Rd PopED/man/feps.add.prop.Rd PopED/man/blockheader.Rd PopED/man/LinMatrixL.Rd PopED/man/getfulld.Rd PopED/man/mf3.Rd PopED/man/ff.PK.1.comp.oral.sd.KE.Rd PopED/man/blockexp.Rd PopED/man/Doptim.Rd PopED/man/poped_optimize.Rd PopED/man/median_hilow_poped.Rd PopED/man/model_prediction.Rd PopED/man/LEDoptim.Rd PopED/man/pargen.Rd PopED/man/LinMatrixL_occ.Rd PopED/man/test_for_min.Rd PopED/man/tic.Rd PopED/man/create.poped.database.Rd PopED/man/summary.poped_optim.Rd PopED/man/ff.PK.1.comp.oral.md.CL.Rd PopED/man/a_line_search.Rd PopED/man/getTruncatedNormal.Rd PopED/man/mfea.Rd PopED/man/ed_laplace_ofv.Rd PopED/man/test_mat_size.Rd PopED/man/mftot7.Rd PopED/man/evaluate_design.Rd PopED/man/blockopt.Rd PopED/man/randn.Rd PopED/man/evaluate.e.ofv.fim.Rd PopED/man/feps.add.Rd PopED/man/get_all_params.Rd PopED/man/plot_efficiency_of_windows.Rd PopED/man/mftot6.Rd PopED/man/ff.PKPD.1.comp.oral.md.CL.imax.Rd PopED/man/size.Rd PopED/man/feval.Rd PopED/man/mf6.Rd PopED/man/isfield.Rd PopED/man/mc_mean.Rd PopED/man/RS_opt.Rd PopED/man/ff.PK.1.comp.oral.sd.CL.Rd PopED/man/mftot4.Rd PopED/man/gradf_eps.Rd PopED/man/optim_ARS.Rd PopED/man/cell.Rd PopED/man/poped.choose.Rd PopED/man/inv.Rd PopED/man/efficiency.Rd PopED/man/ofv_criterion.Rd PopED/man/start_parallel.Rd PopED/man/get_rse.Rd PopED/man/mf5.Rd PopED/man/evaluate.fim.Rd PopED/man/poped_optim.Rd PopED/man/log_prior_pdf.Rd PopED/man/ed_mftot.Rd PopED/man/bfgsb_min.Rd PopED/man/RS_opt_gen.Rd PopED/man/get_unfixed_params.Rd PopED/man/blockfinal.Rd PopED/man/feps.prop.Rd PopED/man/PopED.Rd PopED/man/randperm.Rd PopED/man/diag_matlab.Rd PopED/man/mf7.Rd PopED/man/ofv_fim.Rd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.