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Prints NLME metamodel template file and token json file using given options, filepaths and data

write_ModelTemplateTokens.Rd

This function generates and writes the model template and tokens files based on the provided inputs.

Usage

write_ModelTemplateTokens(
  TemplateFilePath = "template.txt",
  TokensFilePath = "tokens.json",
  Description = "",
  Author = "",
  DataFilePath,
  DataMapping = NULL,
  ColDef = "",
  PMLParametersSets,
  EstArgs = specify_EngineParams(),
  SimArgs = "",
  Tables = list(),
  AppendixRows = "",
  OmegaSearchBlocks = list()
)

Arguments

TemplateFilePath

TemplateFilePath NLME template file path to be written (usually txt).

TokensFilePath

json file path to be written (usually json).

Description

A problem name to be outputted in Description section.

Author

The author information for the model to be outputted in Author section.

DataFilePath

A data file path used by NLME.

DataMapping

Mapping of model terms to data column names, which can be:

  • A named character vector: Used when PMLParametersSets contains a single parameter set. Maps model terms to data columns.

  • A named list of named character vectors: Used when PMLParametersSets contains multiple parameter sets. Each element corresponds to a parameter set, with list names matching the names of PMLParametersSets.

ColDef

A character string specifying additional column definitions in NLME column definition format. See Phoenix NLME documentation for details. https://onlinehelp.certara.com/phoenix/8.6/index.html#t=Phoenix_UserDocs%2FPML%2FColumn_mappings.htm

PMLParametersSets

A list of PML parameters sets (PMLModels class instance).

EstArgs

Estimation arguments for the model template. Please use specify_EngineParams to specify the arguments passed to NLME.

SimArgs

Simulation arguments for the model template. Please use specify_SimParams to specify the arguments passed to NLME.

Tables

A list of Table class instances specifying properties of the tables to be generated after fitting or during simulation.

AppendixRows

Additional rows to include in the model template appendix in NLME column definition format. See Phoenix NLME documentation for details. https://onlinehelp.certara.com/phoenix/8.6/index.html#t=Phoenix_UserDocs%2FPML%2FColumn_mappings.htm

OmegaSearchBlocks

A list of character vectors representing omega names to try to build block omegas.

Value

A list containing statements written to template and tokens files.

Details

Mapping Details:
Basic Mapping: Maps a model variable name (e.g., CObs) to a column name in your data file (e.g., "Concentration").
Shorthand Mapping: If an element is unnamed, the Model Term is assumed to be the same as the Data Column Term. Example: c(ID = "Subject", "Age", Weight = "WT") is equivalent to c(ID = "Subject", Age = "Age", Weight = "WT").
Multiple ID/Grouping Levels: Model terms matching the pattern ID[0-9]? (i.e., ID, ID0, ID1, ID2, ID3, ID4), case-insensitive, are automatically recognized by Certara.RsNLME as NLME sort keys/grouping levels. You can map up to 5 such levels. The function uses these to structure the model execution.
Covariates: If not explicitly mapped, the function attempts to map them using data column names that match covariate names in the model.
Mapping a List: When using a list, each vector must map terms specific to its parameter set, and the list length must equal the number of parameter sets.
Special Terms:

  • Terms <DosepointName>_Duration or <DosepointName>_Rate could be used to map rate/duration columns for the corresponding dosepoints (e.g., A1_Rate = "InfRate"). Term <ObservationName>BQL could be used to map a BQL flag column for the corresponding observation (e.g., CObsBQL = "ConcBQL").

  • The generic AMT term can be used to map the dose amount column; the function will automatically associate it with the primary absorption compartment (e.g., A1 for zero-order/bolus, Aa for first-order) for each parameter set.

  • Generic Duration or Rate terms can be mapped (e.g., Rate = "InfRate"); the function will associate them with the dose mapped via AMT. If a specific mapping like A1_Rate exists, it overrides the generic Rate mapping for that dosepoint (A1).

See also

specify_EngineParams(), specify_SimParams(), Table()

Examples

# Write model template and tokens files
PMLParametersSets <- create_ModelPK(CompartmentsNumber = c(1,2))
# write test data frame
TempFolder <- tempdir()
TemplateFilePath <- file.path(TempFolder, "template.txt")
TokensFilePath <- file.path(TempFolder, "tokens.json")
DataFilePath <- file.path(TempFolder, "Data.csv")
# Ensure data file has columns matching the DataMapping values
write.csv(data.frame(Subject = 'id_1', # Column for ID
                     StudyDay = 1,      # Column for ID1
                     time = 0,         # Column for time
                     DoseAmt = 100,     # Column for AMT
                     Concentration = 10.5, # Column for CObs
                     SubjectAge = 45,   # Column for Age
                     Weight = 70,       # Column for Weight
                     ConcBQL = 0),      # Column for CObsBQL
                     DataFilePath, row.names = FALSE) # Use row.names=FALSE

write_ModelTemplateTokens(
  TemplateFilePath = TemplateFilePath,
  TokensFilePath = TokensFilePath,
  Description = "1-2Cpts try with Multi-ID and Shorthand",
  Author = "Certara",
  DataFilePath = DataFilePath,
  DataMapping = c(ID = "Subject",   # Map ID model term to Subject column
                  ID1 = "StudyDay", # Map ID1 model term to StudyDay column
                  time = "time",    # Map time model term to time column
                  CObs = "Concentration", # Map CObs to Concentration
                  AMT = "DoseAmt",  # Map generic AMT to DoseAmt
                  "SubjectAge",     # Shorthand: Map Age model term to SubjectAge column
                  Weight = "Weight",# Map Weight model term to Weight column
                  CObsBQL = "ConcBQL"), # Map BQL flag
  ColDef = "",
  PMLParametersSets = PMLParametersSets,
  EstArgs = specify_EngineParams(method = "QRPEM"),
  SimArgs = specify_SimParams(numReplicates = 1000L),
  Tables = list(Table(Name = "simtable1.csv",
                      KeepSource = TRUE,
                      VariablesList = "C",
                      ForSimulation = TRUE)),
  OmegaSearchBlocks = list(c("nCl", "nV"), c("nCl2", "nV2")))
#> For method='QRPEM', stdErr must be 'Fisher-Score' or 'None'. Setting stdErr='Fisher-Score'.
#> information stored in C:\Users\jcraig\AppData\Local\Temp\RtmpGQCL5j/template.txt and C:\Users\jcraig\AppData\Local\Temp\RtmpGQCL5j/tokens.json
#> $TokensList
#> $TokensList$PML
#> $TokensList$PML$PK1IVC
#>                                                                                                                                                                                                                                                                                                                                                                                              MAPText 
#>                                                                                                                                                                                                                                                                                                                                                                 " A1 = DoseAmt CObs = Concentration" 
#>                                                                                                                                                                                                                                                                                                                                                                                              PMLText 
#> "test() {\n\tcfMicro(A1, Cl / V)\n\tC = A1 / V\n\tdosepoint(A1, idosevar = A1Dose, infdosevar = A1InfDose, infratevar = A1InfRate)\n\terror(CEps = 0.1)\n\tobserve(CObs = C * (1 + CEps))\n\t\n\tstparm(Cl = tvCl * exp( nCl ))\n\tfixef(tvCl= c(, 1, ))\n\tranef(diag(nCl) = c(1))\n\tstparm(V = tvV * exp( nV ))\n\tfixef(tvV= c(, 1, ))\n\tranef(diag(nV) = c(1))\n\n\t#search_block(nCl, nV)\n}" 
#> 
#> $TokensList$PML$PK2IVC
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            MAPText 
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               " A1 = DoseAmt CObs = Concentration" 
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            PMLText 
#> "test() {\n\tcfMicro(A1, Cl / V, Cl2 / V, Cl2 / V2)\nC = A1 / V\n\tdosepoint(A1, idosevar = A1Dose, infdosevar = A1InfDose, infratevar = A1InfRate)\n\terror(CEps = 0.1)\n\tobserve(CObs = C * (1 + CEps))\n\t\n\tstparm(Cl = tvCl * exp( nCl ))\n\tfixef(tvCl= c(, 1, ))\n\tranef(diag(nCl) = c(1))\n\tstparm(V = tvV * exp( nV ))\n\tfixef(tvV= c(, 1, ))\n\tranef(diag(nV) = c(1))\n\tstparm(Cl2 = tvCl2 * exp( nCl2 ))\n\tfixef(tvCl2= c(, 1, ))\n\tranef(diag(nCl2) = c(1))\n\tstparm(V2 = tvV2 * exp( nV2 ))\n\tfixef(tvV2= c(, 1, ))\n\tranef(diag(nV2) = c(1))\n\n\t#search_block(nCl, nV)\n\t#search_block(nCl2, nV2)\n}" 
#> 
#> 
#> 
#> $Template
#> $Template$Description
#> [1] "##Description: 1-2Cpts try with Multi-ID and Shorthand"
#> 
#> $Template$Author
#> [1] "##Author: Certara"
#> 
#> $Template$DATA
#> [1] "##DATA {data_dir}/Data.csv"
#> 
#> $Template$MAP
#> [1] "##MAP   {PML[1]} ID = Subject ID1 = StudyDay time = time SubjectAge = SubjectAge Weight = Weight CObsBQL = ConcBQL"
#> 
#> $Template$MODEL
#> [1] "##MODEL {PML[2]}"
#> 
#> $Template$ESTARGS
#> [1] "##ESTARGS\n sort=FALSE method=QRPEM"
#> 
#> $Template$SIMARGS
#> [1] "##SIMARGS\n numReplicates=1000 seed=1234 sort=FALSE"
#> 
#> $Template$TABLES
#> [1] "##TABLES\nsimtbl(file=\"simtable1.csv\", C, mode = keep)\n"
#> 
#> 

# Multiple parameter sets
PMLParametersSets <- create_ModelPK(Absorption =c("Intravenous", "Weibull"))
DataMapping <- list(
  c(ID = "Subject", time = "time", Aa = "DoseAmt", CObs = "Concentration"),
  c(ID = "Subject", time = "time", A1 = "DoseAmt", CObs = "Concentration")
)

names(DataMapping) <- names(PMLParametersSets)

write_ModelTemplateTokens(
  TemplateFilePath = TemplateFilePath,
  TokensFilePath = TokensFilePath,
  Description = "1 Cpt Weibull and First-Order",
  Author = "Certara",
  DataFilePath = DataFilePath,
  DataMapping = DataMapping,
  PMLParametersSets = PMLParametersSets)
#> Cannot map A1 for PK1IVC since there's no corresponding mapping name given.
#> information stored in C:\Users\jcraig\AppData\Local\Temp\RtmpGQCL5j/template.txt and C:\Users\jcraig\AppData\Local\Temp\RtmpGQCL5j/tokens.json
#> $TokensList
#> $TokensList$PML
#> $TokensList$PML$PK1IVC
#>                                                                                                                                                                                                                                                                                                                                                                    MAPText 
#>                                                                                                                                                                                                                                                                                                                          "  CObs = Concentration ID = Subject time = time" 
#>                                                                                                                                                                                                                                                                                                                                                                    PMLText 
#> "test() {\n\tcfMicro(A1, Cl / V)\n\tC = A1 / V\n\tdosepoint(A1, idosevar = A1Dose, infdosevar = A1InfDose, infratevar = A1InfRate)\n\terror(CEps = 0.1)\n\tobserve(CObs = C * (1 + CEps))\n\t\n\tstparm(Cl = tvCl * exp( nCl ))\n\tfixef(tvCl= c(, 1, ))\n\tranef(diag(nCl) = c(1))\n\tstparm(V = tvV * exp( nV ))\n\tfixef(tvV= c(, 1, ))\n\tranef(diag(nV) = c(1))\n\n}" 
#> 
#> $TokensList$PML$PK1WC
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      MAPText 
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               "  A1 = DoseAmt CObs = Concentration ID = Subject time = time" 
#>                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      PMLText 
#> "test() {\n\tdelayInfCpt(A1, MeanDelayTime, ShapeParamMinusOne, out = - Cl * C, dist = Weibull)\n\tC = A1 / V\n\tdosepoint(A1, idosevar = A1Dose, infdosevar = A1InfDose, infratevar = A1InfRate)\n\terror(CEps = 0.1)\n\tobserve(CObs = C * (1 + CEps))\n\t\n\tstparm(MeanDelayTime = tvMeanDelayTime * exp( nMeanDelayTime ))\n\tfixef(tvMeanDelayTime= c(, 1, ))\n\tranef(diag(nMeanDelayTime) = c(1))\n\tstparm(ShapeParamMinusOne = tvShapeParamMinusOne * exp( nShapeParamMinusOne ))\n\tfixef(tvShapeParamMinusOne= c(, 1, ))\n\tranef(diag(nShapeParamMinusOne) = c(1))\n\tstparm(Cl = tvCl * exp( nCl ))\n\tfixef(tvCl= c(, 1, ))\n\tranef(diag(nCl) = c(1))\n\tstparm(V = tvV * exp( nV ))\n\tfixef(tvV= c(, 1, ))\n\tranef(diag(nV) = c(1))\n\n}" 
#> 
#> 
#> 
#> $Template
#> $Template$Description
#> [1] "##Description: 1 Cpt Weibull and First-Order"
#> 
#> $Template$Author
#> [1] "##Author: Certara"
#> 
#> $Template$DATA
#> [1] "##DATA {data_dir}/Data.csv"
#> 
#> $Template$MAP
#> [1] "##MAP {PML[1]}"
#> 
#> $Template$MODEL
#> [1] "##MODEL {PML[2]}"
#> 
#> $Template$ESTARGS
#> [1] "##ESTARGS\n sort=FALSE"
#> 
#> $Template$TABLES
#> [1] "##TABLES\n"
#> 
#>