Skip to contents

Create a PopED database

Source: R/create.poped.database.R
create.poped.database.Rd

This function takes the input file (a previously created poped database) supplied by the user, or function arguments, and creates a database that can then be used to run all other PopED functions. The function supplies default values to elements of the database that are not specified in the input file or as function arguments. Default arguments are supplied in the Usage section (easiest to use a text search to find values you are interested in).

Usage

create.poped.database(
  popedInput = list(),
  ff_file = NULL,
  ff_fun = poped.choose(popedInput$model$ff_pointer, NULL),
  fg_file = NULL,
  fg_fun = poped.choose(popedInput$model$fg_pointer, NULL),
  fError_file = NULL,
  fError_fun = poped.choose(popedInput$model$ferror_pointer, NULL),
  optsw = poped.choose(popedInput$settings$optsw, cbind(0, 0, 0, 0, 0)),
  xt = poped.choose(popedInput$design[["xt"]], stop("'xt' needs to be defined")),
  m = poped.choose(popedInput$design[["m"]], NULL),
  x = poped.choose(popedInput$design[["x"]], NULL),
  nx = poped.choose(popedInput$design$nx, NULL),
  a = poped.choose(popedInput$design[["a"]], NULL),
  groupsize = poped.choose(popedInput$design$groupsize,
    stop("'groupsize' needs to be defined")),
  ni = poped.choose(popedInput$design$ni, NULL),
  model_switch = poped.choose(popedInput$design$model_switch, NULL),
  maxni = poped.choose(popedInput$design_space$maxni, NULL),
  minni = poped.choose(popedInput$design_space$minni, NULL),
  maxtotni = poped.choose(popedInput$design_space$maxtotni, NULL),
  mintotni = poped.choose(popedInput$design_space$mintotni, NULL),
  maxgroupsize = poped.choose(popedInput$design_space$maxgroupsize, NULL),
  mingroupsize = poped.choose(popedInput$design_space$mingroupsize, NULL),
  maxtotgroupsize = poped.choose(popedInput$design_space$maxtotgroupsize, NULL),
  mintotgroupsize = poped.choose(popedInput$design_space$mintotgroupsize, NULL),
  maxxt = poped.choose(popedInput$design_space$maxxt, NULL),
  minxt = poped.choose(popedInput$design_space$minxt, NULL),
  discrete_xt = poped.choose(popedInput$design_space$xt_space, NULL),
  discrete_x = poped.choose(popedInput$design_space$discrete_x, NULL),
  maxa = poped.choose(popedInput$design_space$maxa, NULL),
  mina = poped.choose(popedInput$design_space$mina, NULL),
  discrete_a = poped.choose(popedInput$design_space$a_space, NULL),
  bUseGrouped_xt = poped.choose(popedInput$design_space$bUseGrouped_xt, FALSE),
  G_xt = poped.choose(popedInput$design_space$G_xt, NULL),
  bUseGrouped_a = poped.choose(popedInput$design_space$bUseGrouped_a, FALSE),
  G_a = poped.choose(popedInput$design_space$G_a, NULL),
  bUseGrouped_x = poped.choose(popedInput$design_space$bUseGrouped_x, FALSE),
  G_x = poped.choose(popedInput$design_space[["G_x"]], NULL),
  iFIMCalculationType = poped.choose(popedInput$settings$iFIMCalculationType, 1),
  iApproximationMethod = poped.choose(popedInput$settings$iApproximationMethod, 0),
  iFOCENumInd = poped.choose(popedInput$settings$iFOCENumInd, 1000),
  prior_fim = poped.choose(popedInput$settings$prior_fim, matrix(0, 0, 1)),
  strAutoCorrelationFile = poped.choose(popedInput$model$auto_pointer, ""),
  d_switch = poped.choose(popedInput$settings$d_switch, 1),
  ofv_calc_type = poped.choose(popedInput$settings$ofv_calc_type, 4),
  ds_index = popedInput$parameters$ds_index,
  strEDPenaltyFile = poped.choose(popedInput$settings$strEDPenaltyFile, ""),
  ofv_fun = poped.choose(popedInput$settings$ofv_fun, NULL),
  iEDCalculationType = poped.choose(popedInput$settings$iEDCalculationType, 0),
  ED_samp_size = poped.choose(popedInput$settings$ED_samp_size, 45),
  bLHS = poped.choose(popedInput$settings$bLHS, 1),
  strUserDistributionFile = poped.choose(popedInput$model$user_distribution_pointer, ""),
  nbpop = popedInput$parameters$nbpop,
  NumRanEff = popedInput$parameters$NumRanEff,
  NumDocc = popedInput$parameters$NumDocc,
  NumOcc = popedInput$parameters$NumOcc,
  bpop = poped.choose(popedInput$parameters$bpop, stop("bpop must be defined")),
  d = poped.choose(popedInput$parameters$d, NULL),
  covd = popedInput$parameters$covd,
  sigma = popedInput$parameters$sigma,
  docc = poped.choose(popedInput$parameters$docc, matrix(0, 0, 3)),
  covdocc = poped.choose(popedInput$parameters$covdocc, zeros(1, length(docc[, 2, drop =
    F]) * (length(docc[, 2, drop = F]) - 1)/2)),
  notfixed_bpop = popedInput$parameters$notfixed_bpop,
  notfixed_d = popedInput$parameters$notfixed_d,
  notfixed_covd = popedInput$parameters$notfixed_covd,
  notfixed_docc = popedInput$parameters$notfixed_docc,
  notfixed_covdocc = poped.choose(popedInput$parameters$notfixed_covdocc, zeros(1,
    length(covdocc))),
  notfixed_sigma = poped.choose(popedInput$parameters$notfixed_sigma, t(rep(1,
    size(sigma, 2)))),
  notfixed_covsigma = poped.choose(popedInput$parameters$notfixed_covsigma, zeros(1,
    length(notfixed_sigma) * (length(notfixed_sigma) - 1)/2)),
  reorder_parameter_vectors = FALSE,
  bUseRandomSearch = poped.choose(popedInput$settings$bUseRandomSearch, TRUE),
  bUseStochasticGradient = poped.choose(popedInput$settings$bUseStochasticGradient, TRUE),
  bUseLineSearch = poped.choose(popedInput$settings$bUseLineSearch, TRUE),
  bUseExchangeAlgorithm = poped.choose(popedInput$settings$bUseExchangeAlgorithm, FALSE),
  bUseBFGSMinimizer = poped.choose(popedInput$settings$bUseBFGSMinimizer, FALSE),
  EACriteria = poped.choose(popedInput$settings$EACriteria, 1),
  strRunFile = poped.choose(popedInput$settings$run_file_pointer, ""),
  poped_version = poped.choose(popedInput$settings$poped_version,
    packageVersion("PopED")),
  modtit = poped.choose(popedInput$settings$modtit, "PopED model"),
  output_file = poped.choose(popedInput$settings$output_file, paste("PopED_output",
    "_summary", sep = "")),
  output_function_file = poped.choose(popedInput$settings$output_function_file,
    paste("PopED", "_output_", sep = "")),
  strIterationFileName = poped.choose(popedInput$settings$strIterationFileName,
    paste("PopED", "_current.R", sep = "")),
  user_data = poped.choose(popedInput$settings$user_data, cell(0, 0)),
  ourzero = poped.choose(popedInput$settings$ourzero, 1e-05),
  dSeed = poped.choose(popedInput$settings$dSeed, NULL),
  line_opta = poped.choose(popedInput$settings$line_opta, NULL),
  line_optx = poped.choose(popedInput$settings$line_optx, NULL),
  bShowGraphs = poped.choose(popedInput$settings$bShowGraphs, FALSE),
  use_logfile = poped.choose(popedInput$settings$use_logfile, FALSE),
  m1_switch = poped.choose(popedInput$settings$m1_switch, 1),
  m2_switch = poped.choose(popedInput$settings$m2_switch, 1),
  hle_switch = poped.choose(popedInput$settings$hle_switch, 1),
  gradff_switch = poped.choose(popedInput$settings$gradff_switch, 1),
  gradfg_switch = poped.choose(popedInput$settings$gradfg_switch, 1),
  grad_all_switch = poped.choose(popedInput$settings$grad_all_switch, 1),
  rsit_output = poped.choose(popedInput$settings$rsit_output, 5),
  sgit_output = poped.choose(popedInput$settings$sgit_output, 1),
  hm1 = poped.choose(popedInput$settings[["hm1"]], 1e-05),
  hlf = poped.choose(popedInput$settings[["hlf"]], 1e-05),
  hlg = poped.choose(popedInput$settings[["hlg"]], 1e-05),
  hm2 = poped.choose(popedInput$settings[["hm2"]], 1e-05),
  hgd = poped.choose(popedInput$settings[["hgd"]], 1e-05),
  hle = poped.choose(popedInput$settings[["hle"]], 1e-05),
  AbsTol = poped.choose(popedInput$settings$AbsTol, 1e-06),
  RelTol = poped.choose(popedInput$settings$RelTol, 1e-06),
  iDiffSolverMethod = poped.choose(popedInput$settings$iDiffSolverMethod, NULL),
  bUseMemorySolver = poped.choose(popedInput$settings$bUseMemorySolver, FALSE),
  rsit = poped.choose(popedInput$settings[["rsit"]], 300),
  sgit = poped.choose(popedInput$settings[["sgit"]], 150),
  intrsit = poped.choose(popedInput$settings$intrsit, 250),
  intsgit = poped.choose(popedInput$settings$intsgit, 50),
  maxrsnullit = poped.choose(popedInput$settings$maxrsnullit, 50),
  convergence_eps = poped.choose(popedInput$settings$convergence_eps, 1e-08),
  rslxt = poped.choose(popedInput$settings$rslxt, 10),
  rsla = poped.choose(popedInput$settings$rsla, 10),
  cfaxt = poped.choose(popedInput$settings$cfaxt, 0.001),
  cfaa = poped.choose(popedInput$settings$cfaa, 0.001),
  bGreedyGroupOpt = poped.choose(popedInput$settings$bGreedyGroupOpt, FALSE),
  EAStepSize = poped.choose(popedInput$settings$EAStepSize, 0.01),
  EANumPoints = poped.choose(popedInput$settings$EANumPoints, FALSE),
  EAConvergenceCriteria = poped.choose(popedInput$settings$EAConvergenceCriteria, 1e-20),
  bEANoReplicates = poped.choose(popedInput$settings$bEANoReplicates, FALSE),
  BFGSConvergenceCriteriaMinStep = NULL,
  BFGSProjectedGradientTol = poped.choose(popedInput$settings$BFGSProjectedGradientTol,
    1e-04),
  BFGSTolerancef = poped.choose(popedInput$settings$BFGSTolerancef, 0.001),
  BFGSToleranceg = poped.choose(popedInput$settings$BFGSToleranceg, 0.9),
  BFGSTolerancex = poped.choose(popedInput$settings$BFGSTolerancex, 0.1),
  ED_diff_it = poped.choose(popedInput$settings$ED_diff_it, 30),
  ED_diff_percent = poped.choose(popedInput$settings$ED_diff_percent, 10),
  line_search_it = poped.choose(popedInput$settings$ls_step_size, 50),
  Doptim_iter = poped.choose(popedInput$settings$iNumSearchIterationsIfNotLineSearch, 1),
  iCompileOption = poped.choose(popedInput$settings$parallel$iCompileOption, -1),
  iUseParallelMethod = poped.choose(popedInput$settings$parallel$iUseParallelMethod, 1),
  MCC_Dep = NULL,
  strExecuteName = poped.choose(popedInput$settings$parallel$strExecuteName,
    "calc_fim.exe"),
  iNumProcesses = poped.choose(popedInput$settings$parallel$iNumProcesses, 2),
  iNumChunkDesignEvals = poped.choose(popedInput$settings$parallel$iNumChunkDesignEvals,
    -2),
  Mat_Out_Pre = poped.choose(popedInput$settings$parallel$strMatFileOutputPrefix,
    "parallel_output"),
  strExtraRunOptions = poped.choose(popedInput$settings$parallel$strExtraRunOptions, ""),
  dPollResultTime = poped.choose(popedInput$settings$parallel$dPollResultTime, 0.1),
  strFunctionInputName = poped.choose(popedInput$settings$parallel$strFunctionInputName,
    "function_input"),
  bParallelRS = poped.choose(popedInput$settings$parallel$bParallelRS, FALSE),
  bParallelSG = poped.choose(popedInput$settings$parallel$bParallelSG, FALSE),
  bParallelMFEA = poped.choose(popedInput$settings$parallel$bParallelMFEA, FALSE),
  bParallelLS = poped.choose(popedInput$settings$parallel$bParallelLS, FALSE)
)

Arguments

popedInput

A PopED database file or an empty list list(). List elements should match the values seen in the Usage section (the defaults to function arguments).

ff_file

  • ******START OF MODEL DEFINITION OPTIONS**********

A string giving the function name or filename and path of the structural model. The filename and the function name must be the same if giving a filename. e.g. "ff.PK.1.comp.oral.md.KE"

ff_fun

Function describing the structural model. e.g. ff.PK.1.comp.oral.md.KE.

fg_file

A string giving the function name or filename and path of the parameter model. The filename and the function name must be the same if giving a filename. e.g. "parameter.model"

fg_fun

Function describing the parameter model. e.g. parameter.model.

fError_file

A string giving the function name or filename and path of the residual error model. The filename and the function name must be the same if giving a filename. e.g. "feps.prop".

fError_fun

Function describing the residual error model. e.g. feps.prop.

optsw

  • ******WHAT TO OPTIMIZE**********

Row vector of optimization tasks (1=TRUE,0=FALSE) in the following order: (Samples per subject, Sampling schedule, Discrete design variable, Continuous design variable, Number of id per group). All elements set to zero => only calculate the FIM with current design

xt

  • ******START OF INITIAL DESIGN OPTIONS**********

Matrix defining the initial sampling schedule. Each row is a group/individual. If only one vector is supplied, e.g. c(1,2,3,4), then all groups will have the same initial design.

m

Number of groups in the study. Each individual in a group will have the same design.

x

A matrix defining the initial discrete values for the model Each row is a group/individual.

nx

Number of discrete design variables.

a

Matrix defining the initial continuous covariate values. n_rows=number of groups, n_cols=number of covariates. If the number of rows is one and the number of groups > 1 then all groups are assigned the same values.

groupsize

Vector defining the size of the different groups (num individuals in each group). If only one number then the number will be the same in every group.

ni

Vector defining the number of samples for each group.

model_switch

Matrix defining which response a certain sampling time belongs to.

maxni

  • ******START OF DESIGN SPACE OPTIONS**********

Max number of samples per group/individual

minni

Min number of samples per group/individual

maxtotni

Number defining the maximum number of samples allowed in the experiment.

mintotni

Number defining the minimum number of samples allowed in the experiment.

maxgroupsize

Vector defining the max size of the different groups (max number of individuals in each group)

mingroupsize

Vector defining the min size of the different groups (min num individuals in each group) –

maxtotgroupsize

The total maximal groupsize over all groups

mintotgroupsize

The total minimal groupsize over all groups

maxxt

Matrix or single value defining the maximum value for each xt sample. If a single value is supplied then all xt values are given the same maximum value.

minxt

Matrix or single value defining the minimum value for each xt sample. If a single value is supplied then all xt values are given the same minimum value

discrete_xt

Cell array cell defining the discrete variables allowed for each xt value. Can also be a list of values list(1:10) (same values allowed for all xt), or a list of lists list(1:10, 2:23, 4:6) (one for each value in xt). See examples in create_design_space.

discrete_x

Cell array defining the discrete variables for each x value. See examples in create_design_space.

maxa

Vector defining the max value for each covariate. If a single value is supplied then all a values are given the same max value

mina

Vector defining the min value for each covariate. If a single value is supplied then all a values are given the same max value

discrete_a

Cell array cell defining the discrete variables allowed for each a value. Can also be a list of values list(1:10) (same values allowed for all a), or a list of lists list(1:10, 2:23, 4:6) (one for each value in a). See examples in create_design_space.

bUseGrouped_xt

Use grouped time points (1=TRUE, 0=FALSE).

G_xt

Matrix defining the grouping of sample points. Matching integers mean that the points are matched.

bUseGrouped_a

Use grouped covariates (1=TRUE, 0=FALSE)

G_a

Matrix defining the grouping of covariates. Matching integers mean that the points are matched.

bUseGrouped_x

Use grouped discrete design variables (1=TRUE, 0=FALSE).

G_x

Matrix defining the grouping of discrete design variables. Matching integers mean that the points are matched.

iFIMCalculationType

  • ******START OF FIM CALCULATION OPTIONS**********

Fisher Information Matrix type

  • 0=Full FIM

  • 1=Reduced FIM

  • 2=weighted models

  • 3=Loc models

  • 4=reduced FIM with derivative of SD of sigma as in PFIM

  • 5=FULL FIM parameterized with A,B,C matrices & derivative of variance

  • 6=Calculate one model switch at a time, good for large matrices

  • 7=Reduced FIM parameterized with A,B,C matrices & derivative of variance

iApproximationMethod

Approximation method for model, 0=FO, 1=FOCE, 2=FOCEI, 3=FOI

iFOCENumInd

Num individuals in each step of FOCE

prior_fim

The prior FIM (added to calculated FIM)

strAutoCorrelationFile

Filename and path, or function name, for the Autocorrelation function, empty string means no autocorrelation.

d_switch

  • ******START OF CRITERION SPECIFICATION OPTIONS**********

D-family design (1) or ED-family design (0) (with or without parameter uncertainty)

ofv_calc_type

OFV calculation type for FIM

  • 1 = "D-optimality". Determinant of the FIM: det(FIM)

  • 2 = "A-optimality". Inverse of the sum of the expected parameter variances: 1/trace_matrix(inv(FIM))

  • 4 = "lnD-optimality". Natural logarithm of the determinant of the FIM: log(det(FIM))

  • 6 = "Ds-optimality". Ratio of the Determinant of the FIM and the Determinant of the uninteresting rows and columns of the FIM: det(FIM)/det(FIM_u)

  • 7 = Inverse of the sum of the expected parameter RSE: 1/sum(get_rse(FIM,poped.db,use_percent=FALSE))

ds_index

Ds_index is a vector set to 1 if a parameter is uninteresting, otherwise 0. size=(1,num unfixed parameters). First unfixed bpop, then unfixed d, then unfixed docc and last unfixed sigma. Default is the fixed effects being important, everything else not important. Used in conjunction with ofv_calc_type=6.

strEDPenaltyFile

Penalty function name or path and filename, empty string means no penalty. User defined criterion can be defined this way.

ofv_fun

User defined function used to compute the objective function. The function must have a poped database object as its first argument and have "..." in its argument list. Can be referenced as a function or as a file name where the function defined in the file has the same name as the file. e.g. "cost.txt" has a function named "cost" in it.

iEDCalculationType

  • ******START OF E-FAMILY CRITERION SPECIFICATION OPTIONS**********

ED Integral Calculation, 0=Monte-Carlo-Integration, 1=Laplace Approximation, 2=BFGS Laplace Approximation – –

ED_samp_size

Sample size for E-family sampling

bLHS

How to sample from distributions in E-family calculations. 0=Random Sampling, 1=LatinHyperCube –

strUserDistributionFile

Filename and path, or function name, for user defined distributions for E-family designs

nbpop

  • ******START OF Model parameters SPECIFICATION OPTIONS**********

Number of typical values

NumRanEff

Number of IIV parameters. Typically can be computed from other values and not supplied.

NumDocc

Number of IOV variance parameters. Typically can be computed from other values and not supplied.

NumOcc

Number of occasions. Typically can be computed from other values and not supplied.

bpop

Matrix defining the fixed effects, per row (row number = parameter_number) we should have:

  • column 1 the type of the distribution for E-family designs (0 = Fixed, 1 = Normal, 2 = Uniform, 3 = User Defined Distribution, 4 = lognormal and 5 = truncated normal)

  • column 2 defines the mean.

  • column 3 defines the variance of the distribution (or length of uniform distribution).

Can also just supply the parameter values as a vector c() if no uncertainty around the parameter value is to be used. The parameter order of 'bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named arguments in 'bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. See `reorder_parameter_vectors`.

d

Matrix defining the diagonals of the IIV (same logic as for the fixed effects matrix bpop to define uncertainty). One can also just supply the parameter values as a c(). The parameter order of 'd' is defined in the 'fg_fun' or 'fg_file'. If you use named arguments in 'd' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. See `reorder_parameter_vectors`.

covd

Column major vector defining the covariances of the IIV variances. That is, from your full IIV matrix covd <- IIV[lower.tri(IIV)].

sigma

Matrix defining the variances can covariances of the residual variability terms of the model. can also just supply the diagonal parameter values (variances) as a c().

docc

Matrix defining the IOV, the IOV variances and the IOV distribution as for d and bpop.

covdocc

Column major vector defining the covariance of the IOV, as in covd.

notfixed_bpop

  • ******START OF Model parameters fixed or not SPECIFICATION OPTIONS**********

Vector defining if a typical value is fixed or not (1=not fixed, 0=fixed). The parameter order of 'notfixed_bpop' is defined in the 'fg_fun' or 'fg_file'. If you use named arguments in 'notfixed_bpop' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. See `reorder_parameter_vectors`.

notfixed_d

Vector defining if a IIV is fixed or not (1=not fixed, 0=fixed). The parameter order of 'notfixed_d' is defined in the 'fg_fun' or 'fg_file'. If you use named arguments in 'notfixed_d' then the order of this vector can be rearranged to match the 'fg_fun' or 'fg_file'. See `reorder_parameter_vectors`. .

notfixed_covd

Vector defining if a covariance IIV is fixed or not (1=not fixed, 0=fixed)

notfixed_docc

Vector defining if an IOV variance is fixed or not (1=not fixed, 0=fixed)

notfixed_covdocc

Vector row major order for lower triangular matrix defining if a covariance IOV is fixed or not (1=not fixed, 0=fixed)

notfixed_sigma

Vector defining if a residual error parameter is fixed or not (1=not fixed, 0=fixed)

notfixed_covsigma

Vector defining if a covariance residual error parameter is fixed or not (1=not fixed, 0=fixed). Default is fixed.

reorder_parameter_vectors

If you use named arguments in 'bpop' or 'd' then PopED will try to figure out the order of the parameters based on what is found in the 'fg_fun'. See the resulting `poped_db$parameters` and make sure the order matches with 'fg_fun'.

bUseRandomSearch

  • ******START OF Optimization algorithm SPECIFICATION OPTIONS**********

Use random search (1=TRUE, 0=FALSE)

bUseStochasticGradient

Use Stochastic Gradient search (1=TRUE, 0=FALSE)

bUseLineSearch

Use Line search (1=TRUE, 0=FALSE)

bUseExchangeAlgorithm

Use Exchange algorithm (1=TRUE, 0=FALSE)

bUseBFGSMinimizer

Use BFGS Minimizer (1=TRUE, 0=FALSE)

EACriteria

Exchange Algorithm Criteria, 1 = Modified, 2 = Fedorov

strRunFile

Filename and path, or function name, for a run file that is used instead of the regular PopED call.

poped_version

  • ******START OF Labeling and file names SPECIFICATION OPTIONS**********

The current PopED version

modtit

The model title

output_file

Filename and path of the output file during search

output_function_file

Filename suffix of the result function file

strIterationFileName

Filename and path for storage of current optimal design

user_data

  • ******START OF Miscellaneous SPECIFICATION OPTIONS**********

User defined data structure that, for example could be used to send in data to the model

ourzero

Value to interpret as zero in design

dSeed

The seed number used for optimization and sampling – integer or -1 which creates a random seed as.integer(Sys.time()) or NULL.

line_opta

Vector for line search on continuous design variables (1=TRUE,0=FALSE)

line_optx

Vector for line search on discrete design variables (1=TRUE,0=FALSE)

bShowGraphs

Use graph output during search

use_logfile

If a log file should be used (0=FALSE, 1=TRUE)

m1_switch

Method used to calculate M1 (0=Complex difference, 1=Central difference, 20=Analytic derivative, 30=Automatic differentiation)

m2_switch

Method used to calculate M2 (0=Central difference, 1=Central difference, 20=Analytic derivative, 30=Automatic differentiation)

hle_switch

Method used to calculate linearization of residual error (0=Complex difference, 1=Central difference, 30=Automatic differentiation)

gradff_switch

Method used to calculate the gradient of the model (0=Complex difference, 1=Central difference, 20=Analytic derivative, 30=Automatic differentiation)

gradfg_switch

Method used to calculate the gradient of the parameter vector g (0=Complex difference, 1=Central difference, 20=Analytic derivative, 30=Automatic differentiation)

grad_all_switch

Method used to calculate all the gradients (0=Complex difference, 1=Central difference)

rsit_output

Number of iterations in random search between screen output

sgit_output

Number of iterations in stochastic gradient search between screen output

hm1

Step length of derivative of linearized model w.r.t. typical values

hlf

Step length of derivative of model w.r.t. g

hlg

Step length of derivative of g w.r.t. b

hm2

Step length of derivative of variance w.r.t. typical values

hgd

Step length of derivative of OFV w.r.t. time

hle

Step length of derivative of model w.r.t. sigma

AbsTol

The absolute tolerance for the diff equation solver

RelTol

The relative tolerance for the diff equation solver

iDiffSolverMethod

The diff equation solver method, NULL as default.

bUseMemorySolver

If the differential equation results should be stored in memory (1) or not (0)

rsit

Number of Random search iterations

sgit

Number of stochastic gradient iterations

intrsit

Number of Random search iterations with discrete optimization.

intsgit

Number of Stochastic Gradient search iterations with discrete optimization

maxrsnullit

Iterations until adaptive narrowing in random search

convergence_eps

Stochastic Gradient convergence value, (difference in OFV for D-optimal, difference in gradient for ED-optimal)

rslxt

Random search locality factor for sample times

rsla

Random search locality factor for covariates

cfaxt

Stochastic Gradient search first step factor for sample times

cfaa

Stochastic Gradient search first step factor for covariates

bGreedyGroupOpt

Use greedy algorithm for group assignment optimization

EAStepSize

Exchange Algorithm StepSize

EANumPoints

Exchange Algorithm NumPoints

EAConvergenceCriteria

Exchange Algorithm Convergence Limit/Criteria

bEANoReplicates

Avoid replicate samples when using Exchange Algorithm

BFGSConvergenceCriteriaMinStep

BFGS Minimizer Convergence Criteria Minimum Step

BFGSProjectedGradientTol

BFGS Minimizer Convergence Criteria Normalized Projected Gradient Tolerance

BFGSTolerancef

BFGS Minimizer Line Search Tolerance f

BFGSToleranceg

BFGS Minimizer Line Search Tolerance g

BFGSTolerancex

BFGS Minimizer Line Search Tolerance x

ED_diff_it

Number of iterations in ED-optimal design to calculate convergence criteria

ED_diff_percent

ED-optimal design convergence criteria in percent

line_search_it

Number of grid points in the line search

Doptim_iter

Number of iterations of full Random search and full Stochastic Gradient if line search is not used

iCompileOption

******START OF PARALLEL OPTIONS********** Compile options for PopED

  • -1 = No compilation,

  • 0 or 3 = Full compilation,

  • 1 or 4 = Only using MCC (shared lib),

  • 2 or 5 = Only MPI,

  • Option 0,1,2 runs PopED and option 3,4,5 stops after compilation

iUseParallelMethod

Parallel method to use (0 = Matlab PCT, 1 = MPI)

MCC_Dep

Additional dependencies used in MCC compilation (mat-files), if several space separated

strExecuteName

Compilation output executable name

iNumProcesses

Number of processes to use when running in parallel (e.g. 3 = 2 workers, 1 job manager)

iNumChunkDesignEvals

Number of design evaluations that should be evaluated in each process before getting new work from job manager

Mat_Out_Pre

The prefix of the output mat file to communicate with the executable

strExtraRunOptions

Extra options send to e$g. the MPI executable or a batch script, see execute_parallel$m for more information and options

dPollResultTime

Polling time to check if the parallel execution is finished

strFunctionInputName

The file containing the popedInput structure that should be used to evaluate the designs

bParallelRS

If the random search is going to be executed in parallel

bParallelSG

If the stochastic gradient search is going to be executed in parallel

bParallelMFEA

If the modified exchange algorithm is going to be executed in parallel

bParallelLS

If the line search is going to be executed in parallel

Value

A PopED database

See also

Other poped_input: convert_variables(), create_design(), create_design_space(), downsizing_general_design(), poped.choose()

Examples

## Warfarin example from software comparison in:
## Nyberg et al., "Methods and software tools for design evaluation 
##   for population pharmacokinetics-pharmacodynamics studies", 
##   Br. J. Clin. Pharm., 2014. 

library(PopED)

## find the parameters that are needed to define from the structural model
ff.PK.1.comp.oral.md.CL
#> function (model_switch, xt, parameters, poped.db) 
#> {
#>     with(as.list(parameters), {
#>         y = xt
#>         N = floor(xt/TAU) + 1
#>         y = (DOSE * Favail/V) * (KA/(KA - CL/V)) * (exp(-CL/V * 
#>             (xt - (N - 1) * TAU)) * (1 - exp(-N * CL/V * TAU))/(1 - 
#>             exp(-CL/V * TAU)) - exp(-KA * (xt - (N - 1) * TAU)) * 
#>             (1 - exp(-N * KA * TAU))/(1 - exp(-KA * TAU)))
#>         return(list(y = y, poped.db = poped.db))
#>     })
#> }
#> <bytecode: 0x557071c69eb0>
#> <environment: namespace:PopED>

## -- parameter definition function 
## -- names match parameters in function ff
sfg <- function(x,a,bpop,b,bocc){
  parameters=c(CL=bpop[1]*exp(b[1]),
               V=bpop[2]*exp(b[2]),
               KA=bpop[3]*exp(b[3]),
               Favail=bpop[4],
               DOSE=a[1])
    return(parameters) 
}

## -- Define initial design  and design space
poped.db <- create.poped.database(
  ff_fun=ff.PK.1.comp.oral.sd.CL,
  fg_fun=sfg,
  fError_fun=feps.prop,
  bpop=c(CL=0.15, V=8, KA=1.0, Favail=1), 
  notfixed_bpop=c(1,1,1,0),
  d=c(CL=0.07, V=0.02, KA=0.6), 
  sigma=0.01,
  groupsize=32,
  xt=c( 0.5,1,2,6,24,36,72,120),
  minxt=0,
  maxxt=120,
  a=70)


## evaluate initial design
evaluate_design(poped.db)
#> $ofv
#> [1] 52.44799
#> 
#> $fim
#>                     CL          V        KA         d_CL          d_V
#> CL         19821.28445 -21.836551 -8.622140 0.000000e+00     0.000000
#> V            -21.83655  20.656071 -1.807099 0.000000e+00     0.000000
#> KA            -8.62214  -1.807099 51.729039 0.000000e+00     0.000000
#> d_CL           0.00000   0.000000  0.000000 3.107768e+03    10.728786
#> d_V            0.00000   0.000000  0.000000 1.072879e+01 27307.089308
#> d_KA           0.00000   0.000000  0.000000 2.613561e-02     3.265608
#> SIGMA[1,1]     0.00000   0.000000  0.000000 5.215403e+02 11214.210707
#>                   d_KA   SIGMA[1,1]
#> CL          0.00000000      0.00000
#> V           0.00000000      0.00000
#> KA          0.00000000      0.00000
#> d_CL        0.02613561    521.54030
#> d_V         3.26560786  11214.21071
#> d_KA       41.81083599     71.08764
#> SIGMA[1,1] 71.08763902 806176.95068
#> 
#> $rse
#>         CL          V         KA       d_CL        d_V       d_KA SIGMA[1,1] 
#>   4.738266   2.756206  13.925829  25.627205  30.344316  25.777327  11.170784 
#>