Package 'Certara.RsNLME.ModelBuilder'

Run modelBuilderUI() and create resulting metamodel

Description

Used by Pirana to run modelBuilderUI(), saving the resulting metamodel e.g., .mmmdl file given model building operations performed in GUI.

Usage

create_metamodelBuiltin(metamodelFile, datafile, author = "")

Arguments

metamodelFile	File where the metamodel should be created.
datafile	File with input data.
author	Optional character string to specify the author in the metamodel.

Value

NLME PML model S4 class instance

Examples

if (interactive()) {
tmp_data <- tempfile(fileext = ".csv")
write.csv(Certara.RsNLME::pkData, tmp_data, row.names = FALSE)

create_metamodelBuiltin(
  "run1.mmdl",
  tmp_data
  )
}

---

Send metamodel to modelTextualUI() and run shiny application

Description

Used by Pirana to send existing metamodel to modelTextualUI() for editing, and after returning, saves it as a metamodel file e.g, .mmdl.

Usage

create_metamodelTextual(metamodelFile)

Arguments

metamodelFile

Path to existing metmodel file.

Details

If DOSING CYCLE block is presented in the metamodel, it will be transferred to COLDEF block with a warning.

Value

Updated metamodel text.

Examples

if (interactive()) {
mmdl_file <- system.file("vignettesdata/OneCpt_IVInfusion.mmdl",
  package = "Certara.RsNLME")

create_metamodelTextual(
  mmdl_file
  )
}

---

Shiny GUI to examine the model and evaluate estimates for fixed effects.

Description

Shiny GUI to examine the model and evaluate estimates for fixed effects.

Usage

estimatesUI(model, host = NULL)

Arguments

model	Model object.
host	Optional host parameter of class hostParams. If NULL, local host will be used.

Value

A model object of class NlmePmlModel

Examples

if (interactive()) {
library(Certara.RsNLME)
host <- hostParams(
  parallelMethod = "None",
  hostName = "local",
  numCores = 1
)

model <- pkmodel(
  parameterization = "Clearance",
  absorption = "Intravenous",
  numCompartments = 2,
  data = pkData,
  ID = "Subject",
  A1 = "Amount",
  CObs = "Conc",
  Time = "Act_Time",
  modelName = "pk_model"
)

model <- estimatesUI(model, host)
}

---

Build RsNLME model from Shiny GUI and generate corresponding RsNLME code

Description

Shiny application to build RsNLME model from Shiny GUI and generate corresponding RsNLME code based on input selections.

Usage

modelBuilderUI(
  data,
  modelName = "PKPDmodel",
  workingDir = "",
  baseModel = NULL
)

Arguments

data	Input dataset.
modelName	Name of the model; if missing, named as 'PKPDmodel.'
workingDir	Working directory to run the model. Current working directory will be used if workingDir not specified or does not exist.
baseModel	The model object from where the input dataset and model name are recovered if arguments data and modelName are not specified.

Value

A model object of class NlmePmlModel

Examples

if (interactive()) {
model <- modelBuilderUI(data = Certara.RsNLME::pkData, modelName = "PK_Model")
}

---

Edit textual RsNLME model from Shiny GUI

Description

Shiny application to update RsNLME model from Shiny GUI and directly edit PML statements using Ace editor. Syntax and semantic check is performed by TDL executable (if presented). The Shiny application also allows adding input options and column mappings from Shiny GUI.

Usage

modelTextualUI(baseModel, initpml, data, modelName = "PKPDmodel")

Arguments

baseModel	The model object from where the information is recovered.
initpml	Initial PML model file to be edited. Overrides baseModel@statements, if presented.
data	Input data frame. Overrides baseModel@inputData, if presented.
modelName	Name of the model; if missing, named as 'PKPDmodel'. Overrides baseModel@modelInfo@modelName, if presented.

Value

A model object of class NlmePmlModel

Examples

if (interactive()) {
model <- modelBuilderUI(data = Certara.RsNLME::pkData, modelName = "PK_Model")

model <- modelTextualUI(baseModel = model)
}

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