PopED traceback

1PopED_ggplot2_error.md

PopED

traceback

16: stop("Discrete value supplied to continuous scale", call. = FALSE)
15: scales::train_continuous(x, self$range)
14: f(..., self = self)
13: self$range$train(x)
12: f(..., self = self)
11: self$train(df[[aesthetic]])
10: f(..., self = self)
9: scale$train_df(df = df)
8: FUN(X[[i]], ...)
7: lapply(scales$scales, function(scale) scale$train_df(df = df))
6: FUN(X[[i]], ...)
5: lapply(data, scales_train_df, scales = npscales)
4: ggplot_build.ggplot(x)
3: ggplot_build(x)
2: print.ggplot(x)
1: function (x, ...) 
   UseMethod("print")(x)

reprex

system.file("examples", package="PopED")
#> [1] "/Library/Frameworks/R.framework/Versions/3.4/Resources/library/PopED/examples"
library(PopED)
set.seed(1234)
ff <- function(model_switch,xt,parameters,poped.db){
  with(as.list(parameters),{
    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))
  })
}
sfg <- function(x,a,bpop,b,bocc){
  parameters=c( V=bpop[1]*exp(b[1]),
                KA=bpop[2]*exp(b[2]),
                CL=bpop[3]*exp(b[3]),
                Favail=bpop[4],
                DOSE=a[1],
                TAU=a[2])
}
feps <- function(model_switch,xt,parameters,epsi,poped.db){
  returnArgs <- ff(model_switch,xt,parameters,poped.db) 
  y <- returnArgs[[1]]
  poped.db <- returnArgs[[2]]
  
  y = y*(1+epsi[,1])+epsi[,2]
  
  return(list(y=y,poped.db=poped.db)) 
}
poped.db <- create.poped.database(ff_fun=ff,
                                  fg_fun=sfg,
                                  fError_fun=feps,
                                  bpop=c(V=72.8,KA=0.25,CL=3.75,Favail=0.9), 
                                  notfixed_bpop=c(1,1,1,0),
                                  d=c(V=0.09,KA=0.09,CL=0.25^2), 
                                  sigma=c(0.04,5e-6),
                                  notfixed_sigma=c(1,0),
                                  m=2,
                                  groupsize=20,
                                  a=list(c(DOSE=20,TAU=24),c(DOSE=40, TAU=24)),
                                  maxa=c(DOSE=200,TAU=24),
                                  mina=c(DOSE=0,TAU=24),
                                  xt=c( 1,2,8,240,245),
                                  minxt=c(0,0,0,240,240),
                                  maxxt=c(10,10,10,248,248),
                                  bUseGrouped_xt=TRUE)
plot_model_prediction(poped.db, model_num_points=500, IPRED=T)
#> Don't know how to automatically pick scale for object of type NULL. Defaulting to continuous.
#> Error: Discrete value supplied to continuous scale

Example from docs works...

## 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

## -- 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_file="ff.PK.1.comp.oral.sd.CL",
                                  fg_file="sfg",
                                  fError_file="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)


plot_model_prediction(poped.db,IPRED=TRUE,DV=TRUE)
#> Don't know how to automatically pick scale for object of type NULL. Defaulting to continuous.

Created on 2018-05-15 by the reprex package (v0.2.0).

Created on 2018-05-15 by the reprex package (v0.2.0).

2popdb_structure.txt

`str(pop.db)`
List of 5
 $ settings    :List of 80
  ..$ poped_version                      :Classes 'package_version', 'numeric_version'  hidden list of 1
  .. ..$ : int [1:3] 0 3 2
  ..$ bLHS                               : num 1
  ..$ d_switch                           : num 1
  ..$ iApproximationMethod               : num 0
  ..$ iFOCENumInd                        : num 1
  ..$ bUseRandomSearch                   : logi TRUE
  ..$ bUseStochasticGradient             : logi TRUE
  ..$ bUseLineSearch                     : logi TRUE
  ..$ bUseExchangeAlgorithm              : logi FALSE
  ..$ bUseBFGSMinimizer                  : logi FALSE
  ..$ iEDCalculationType                 : num 0
  ..$ BFGSConvergenceCriteriaMinStep     : num 1e-08
  ..$ BFGSProjectedGradientTol           : num 1e-04
  ..$ BFGSTolerancef                     : num 0.001
  ..$ BFGSToleranceg                     : num 0.9
  ..$ BFGSTolerancex                     : num 0.1
  ..$ parallel                           :List of 15
  .. ..$ iCompileOption                      : num -1
  .. ..$ strAdditionalMCCCompilerDependencies: chr ""
  .. ..$ iUseParallelMethod                  : num 1
  .. ..$ strExecuteName                      : chr "calc_fim.exe"
  .. ..$ iNumProcesses                       : num 2
  .. ..$ iNumChunkDesignEvals                : num -2
  .. ..$ strMatFileInputPrefix               : chr "parallel_input"
  .. ..$ strMatFileOutputPrefix              : chr "parallel_output"
  .. ..$ strExtraRunOptions                  : chr ""
  .. ..$ dPollResultTime                     : num 0.1
  .. ..$ strFunctionInputName                : chr "function_input"
  .. ..$ bParallelRS                         : logi FALSE
  .. ..$ bParallelSG                         : logi FALSE
  .. ..$ bParallelLS                         : logi FALSE
  .. ..$ bParallelMFEA                       : logi FALSE
  ..$ hm1                                : num 1e-05
  ..$ hlf                                : num 1e-05
  ..$ hlg                                : num 1e-05
  ..$ hm2                                : num 1e-05
  ..$ hgd                                : num 1e-05
  ..$ hle                                : num 1e-05
  ..$ AbsTol                             : num 1e-06
  ..$ RelTol                             : num 1e-06
  ..$ bUseMemorySolver                   : logi FALSE
  ..$ solved_solutions                   : list()
  .. ..- attr(*, "dim")= int [1:2] 0 0
  ..$ maxtime                            : num 248
  ..$ iFIMCalculationType                : num 1
  ..$ rsit                               : num 300
  ..$ sgit                               : num 150
  ..$ intrsit                            : num 250
  ..$ intsgit                            : num 50
  ..$ maxrsnullit                        : num 50
  ..$ convergence_eps                    : num 1e-08
  ..$ rslxt                              : num 10
  ..$ rsla                               : num 10
  ..$ cfaxt                              : num 0.001
  ..$ cfaa                               : num 0.001
  ..$ EACriteria                         : num 1
  ..$ EAStepSize                         : num 0.01
  ..$ EANumPoints                        : logi FALSE
  ..$ EAConvergenceCriteria              : num 1e-20
  ..$ ED_samp_size                       : num 45
  ..$ ED_diff_it                         : num 30
  ..$ ED_diff_percent                    : num 10
  ..$ ls_step_size                       : num 50
  ..$ ofv_calc_type                      : num 4
  ..$ iNumSearchIterationsIfNotLineSearch: num 1
  ..$ ourzero                            : num 1e-05
  ..$ rsit_output                        : num 5
  ..$ sgit_output                        : num 1
  ..$ ed_penalty_pointer                 : num[1, 0 ] 
  ..$ modtit                             : chr "PopED model"
  ..$ exptit                             : chr "PopED model_exp$mat"
  ..$ opttit                             : chr "PopED model_opt$mat"
  ..$ bShowGraphs                        : logi FALSE
  ..$ use_logfile                        : logi FALSE
  ..$ output_file                        : chr "PopED_output_summary"
  ..$ output_function_file               : chr "PopED_output_"
  ..$ optsw                              : num [1, 1:5] 0 0 0 0 0
  ..$ line_opta                          : num [1, 1:2] 1 1
  ..$ line_optx                          : num[1, 0 ] 
  ..$ m1_switch                          : num 1
  ..$ m2_switch                          : num 1
  ..$ hle_switch                         : num 1
  ..$ gradff_switch                      : num 1
  ..$ gradfg_switch                      : num 1
  ..$ prior_fim                          : num[0 , 1] 
  ..$ strIterationFileName               : chr "PopED_current.R"
  ..$ user_data                          : list()
  .. ..- attr(*, "dim")= int [1:2] 0 0
  ..$ bUseSecondOrder                    : logi FALSE
  ..$ bCalculateEBE                      : logi FALSE
  ..$ bGreedyGroupOpt                    : logi FALSE
  ..$ bEANoReplicates                    : logi FALSE
  ..$ run_file_pointer                   : num[1, 0 ] 
  ..$ Engine                             :List of 2
  .. ..$ Type   : num 1
  .. ..$ Version: chr "R version 3.4.3 (2017-11-30)"
  ..$ strOutputFilePath                  : chr "."
  ..$ strOutputFileName                  : chr "PopED_output_summary"
  ..$ strOutputFileExtension             : chr ""
 $ model       :List of 5
  ..$ user_distribution_pointer: chr ""
  ..$ fg_pointer               :function (x, a, bpop, b, bocc)  
  .. ..- attr(*, "srcref")=Class 'srcref'  atomic [1:8] 1 8 10 1 8 1 1 10
  .. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x1168fba30> 
  ..$ auto_pointer             : num[1, 0 ] 
  ..$ ff_pointer               :function (model_switch, xt, parameters, poped.db)  
  .. ..- attr(*, "srcref")=Class 'srcref'  atomic [1:8] 1 7 9 1 7 1 1 9
  .. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x1169c3ab0> 
  ..$ ferror_pointer           :function (model_switch, xt, parameters, epsi, poped.db)  
  .. ..- attr(*, "srcref")=Class 'srcref'  atomic [1:8] 1 9 9 1 9 1 1 9
  .. .. .. ..- attr(*, "srcfile")=Classes 'srcfilecopy', 'srcfile' <environment: 0x11680d808> 
 $ design      :List of 7
  ..$ xt          : num [1:2, 1:5] 1 1 2 2 8 8 240 240 245 245
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr [1:5] "obs_1" "obs_2" "obs_3" "obs_4" ...
  ..$ m           : Named num 2
  .. ..- attr(*, "names")= chr "n_grp"
  ..$ ni          : int [1:2, 1] 5 5
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr "n_obs"
  ..$ model_switch: num [1:2, 1:5] 1 1 1 1 1 1 1 1 1 1
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr [1:5] "obs_1" "obs_2" "obs_3" "obs_4" ...
  ..$ a           : num [1:2, 1:2] 20 40 24 24
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr [1:2] "DOSE" "TAU"
  ..$ groupsize   : num [1:2, 1] 20 20
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr "n_id"
  ..$ x           : num[1:2, 0 ] 
 $ design_space:List of 19
  ..$ maxa           : num [1:2, 1:2] 200 200 24 24
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr [1:2] "DOSE" "TAU"
  ..$ mina           : num [1:2, 1:2] 0 0 24 24
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr [1:2] "DOSE" "TAU"
  ..$ maxni          : int [1:2, 1] 5 5
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr "n_obs"
  ..$ minni          : int [1:2, 1] 5 5
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr "n_obs"
  ..$ maxtotni       : int 10
  ..$ mintotni       : int 10
  ..$ maxgroupsize   : num [1:2, 1] 20 20
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr "n_id"
  ..$ mingroupsize   : num [1:2, 1] 20 20
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr "n_id"
  ..$ maxtotgroupsize: num 40
  ..$ mintotgroupsize: num 40
  ..$ maxxt          : num [1:2, 1:5] 10 10 10 10 10 10 248 248 248 248
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr [1:5] "obs_1" "obs_2" "obs_3" "obs_4" ...
  ..$ minxt          : num [1:2, 1:5] 1.0e-05 1.0e-05 1.0e-05 1.0e-05 1.0e-05 1.0e-05 2.4e+02 2.4e+02 2.4e+02 2.4e+02
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr [1:5] "obs_1" "obs_2" "obs_3" "obs_4" ...
  ..$ bUseGrouped_a  : logi FALSE
  ..$ bUseGrouped_xt : logi TRUE
  ..$ G_a            : num [1:2, 1:2] 1 3 2 4
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr [1:2] "DOSE" "TAU"
  ..$ G_xt           : num [1:2, 1:5] 1 1 2 2 3 3 4 4 5 5
  .. ..- attr(*, "dimnames")=List of 2
  .. .. ..$ : chr [1:2] "grp_1" "grp_2"
  .. .. ..$ : chr [1:5] "obs_1" "obs_2" "obs_3" "obs_4" ...
  ..$ G_x            : num[1:2, 0 ] 
  ..$ bUseGrouped_x  : logi FALSE
  ..$ discrete_x     : list()
  .. ..- attr(*, "dim")= int [1:2] 2 0
 $ parameters  :List of 22
  ..$ covdocc          : num[1, 0 ] 
  ..$ notfixed_covdocc : num[1, 0 ] 
  ..$ notfixed_covsigma: num [1, 1] 0
  ..$ nbpop            : num 4
  ..$ NumRanEff        : num 3
  ..$ NumDocc          : num 0
  ..$ NumOcc           : num 0
  ..$ ng               : int 6
  ..$ notfixed_docc    : num[1, 0 ] 
  ..$ notfixed_d       : num [1, 1:3] 1 1 1
  ..$ notfixed_bpop    : num [1:4] 1 1 1 0
  ..$ covd             : num [1, 1:3] 0 0 0
  ..$ notfixed_covd    : num [1, 1:3] 0 0 0
  ..$ b_global         : num [1:3, 1] 0 0 0
  ..$ bocc_global      :List of 1
  .. ..$ : num[0 , 0 ] 
  .. ..- attr(*, "dim")= int [1:2] 1 1
  ..$ bpop             : num [1:4, 1:3] 0 0 0 0 72.8 0.25 3.75 0.9 0 0 ...
  ..$ d                : num [1:3, 1:3] 0 0 0 0.09 0.09 0.0625 0 0 0
  ..$ sigma            : num [1:2, 1:2] 4e-02 0e+00 0e+00 5e-06
  ..$ docc             : num[0 , 1:3] 
  ..$ notfixed_sigma   : num [1:2] 1 0
  ..$ ds_index         : num [1, 1:7] 0 0 0 1 1 1 1
  ..$ param.pt.val     :List of 4
  .. ..$ bpop : num [1:4, 1] 72.8 0.25 3.75 0.9
  .. ..$ d    : num [1:3, 1:3] 0.09 0 0 0 0.09 0 0 0 0.0625
  .. ..$ docc : num[0 , 0 ] 
  .. ..$ sigma: num [1:2, 1:2] 4e-02 0e+00 0e+00 5e-06