Package 'Certara.ModelResults'

Get eps skrinkage values xpdb

Description

This function returns eps shrinkage values from xpdb object as a data.frame.

Usage

get_eps_shk(xpdb)

Arguments

xpdb	Object of class xpose_data.

Value

Returns an object of class data.frame.

Examples

get_eps_shk(xpdb_NLME$TwCpt_IVBolus_FOCE_ELS)

---

Get eta skrinkage values xpdb

Description

This function returns eta shrinkage values from xpdb object as a data.frame.

Usage

get_eta_shk(xpdb)

Arguments

xpdb	Object of class xpose_data.

Value

Returns an object of class data.frame.

Examples

get_eta_shk(xpdb_NLME$TwCpt_IVBolus_FOCE_ELS)

---

Generate and Report Model Diagnostics from NLME or NONMEM runs

Description

Shiny application to generate, customize, and report diagnostic plots and tables from NLME or NONMEM output files. Create an Rmarkdown file of tagged model diagnostics and render into submission ready report.

Usage

resultsUI(model, xpdb = NULL, tagged = NULL, settings = NULL, ...)

Arguments

model	A single object, vector, or list of objects of class NlmePmlModel.
xpdb	A single object or list of objects of class xpose_data.
tagged	List of tagged objects returned from previous tagged <- resultsUI() session.
settings	List of settings (e.g., settings.Rds) returned from previous Shiny session.
...	Additional arguments for Pirana integration.

Value

If interactive(), returns a list of tagged diagnostics from the Shiny application, otherwise returns TRUE.

Examples

if (interactive()) {


# RsNLME
library(Certara.RsNLME)
library(Certara.ModelResults)

model1 <- pkmodel(numCompartments = 1,
                 data = pkData,
                 ID = "Subject",
                 Time = "Act_Time",
                 A1 = "Amount",
                 CObs = "Conc",
                 modelName = "OneCpt_IVBolus_FOCE-ELS")

baseFitJob1 <- fitmodel(model1)


model2 <- pkmodel(numCompartments = 2,
                 data = pkData,
                 ID = "Subject",
                 Time = "Act_Time",
                 A1 = "Amount",
                 CObs = "Conc",
                 modelName = "TwCpt_IVBolus_FOCE-ELS")

baseFitJob2 <- fitmodel(model2)

# Run Model Results
resultsUI(model = c(model1, model2))


# NONMEM via xpose

library(Certara.ModelResults)
library(xpose)

xpdb <- xpose_data(
  runno = "1",
  prefix = "run",
  ext = ".lst",
  dir = "./NONMEM/Hands_onB/")

resultsUI(xpdb = xpdb)

# Multiple models

xpdb_multiple <- list(
 run1 = xpose_data(file = "run1.lst"),
 run2 = xpose_data(file = "run2.lst"),
 run3 = xpose_data(file = "run3.lst"),
 run4 = xpose_data(file = "run4.lst")
)
}

---

A ggplot2 theme for Certara.

Description

A ggplot2 theme for Certara.

Usage

theme_certara(
  base_size = 11,
  base_family = "",
  base_line_size = base_size/22,
  base_rect_size = base_size/22,
  grid = c("none", "horizontal", "both")
)

Arguments

base_size	base font size, given in pts.
base_family	base font family
base_line_size	base size for line elements
base_rect_size	base size for rect elements
grid	Which grid lines should appear? Horizontal only, both horizontal and vertical, or none (default). continuous_scale().

Details

There are 3 variants of the theme: no grid theme_certara(), full grid theme_certara(grid = "both"), and horizontal grid lines only theme_certara(grid = "horizontal").

Value

An object of class theme().

---

Write code to R script from tagged diagnostics

Description

Use this function to write code to R script from diagnostics tagged in Certara's Model Results Shiny Application.

Usage

write_code(tagged, file)

Arguments

tagged	List of tagged objects from returned from resultsUI().
file	Character specifying path of output file. If missing, it will be saved as code.R in working directory.

Value

Returns NULL after writing to file.

Examples

if (interactive()) {
tagged_diagnostics <- resultsUI(xpdb = xpdb_NLME)

write_code(tagged_diagnostics, "tagged_results.R")

}

---

List of xpose data objects from RsNLME example tutorials

Description

The following object contains a list of 2 xpose_data objects generated in the RsNLME example script TwoCptIVBolus_FitBaseModel_CovariateSearch_VPC_BootStrapping.R.

Usage

xpdb_NLME

Format

List of 2 xpose_data objects constructed from NLME model output.

Details

• xpdb_NLME$`TwCpt_IVBolus_FOCE-ELS` is an xpose_data object created from the base model in RsNLME example script. The model can be used as a reference to compare model diagnostics in final model.

• xpdb_NLME$`TwCpt_IVBolus_SelectedCovariateModel_FOCE-ELS` is an xpose_data object created from the final model in the RsNLME example script. The final model includes selected covariate BodyWeight added from the results of stepwise covariate search.

Source

Certara

---

List of xpose data objects from NONMEM model output

Description

The following object contains of list of 2 xpose_data objects:

Usage

xpdb_NONMEM

Format

List of 2 xpose_data objects constructed from NONMEM model output.

Details

• xpdb_NONMEM$ex_pk is an xpose_data object from xpose::xpdb_ex_pk. The model contains multiple covariates and can be used to explore covariate model diagnostics.

• xpdb_NONMEM$mult_obs is an xpose_data object created from NONMEM model with multiple observed variables. Users will see that appropriate model diagnostic plots are automatically facetted by DVID in the Shiny GUI.

Source

Certara

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