Title: Generate Diagnostics for Pharmacometric Models Using 'shiny'
Version: 3.0.1
Description: Utilize the 'shiny' interface to generate Goodness of Fit (GOF) plots and tables for Non-Linear Mixed Effects (NLME / NONMEM) pharmacometric models. From the interface, users can customize model diagnostics and generate the underlying R code to reproduce the diagnostic plots and tables outside of the 'shiny' session. Model diagnostics can be included in a 'rmarkdown' document and rendered to desired output format.
Depends: R (≥ 4.0)
License: LGPL-3
URL: https://certara.github.io/R-model-results/
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0), Certara.RsNLME
Imports: colourpicker, shinyAce, shinymeta, Certara.Xpose.NLME, xpose, dplyr, flextable, shinyjqui, grDevices, ggplot2, plotly, magrittr, scales, shiny (≥ 1.7.0), shinyjs, shinyWidgets, shinyTree (≥ 0.3.1), sortable, tidyr, rlang, bslib (≥ 0.7.0)
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2025-02-27 23:19:17 UTC; jcraig
Author: James Craig [aut, cre], Shuhua Hu [ctb], Mike Talley [aut], Certara USA, Inc [cph, fnd]
Maintainer: James Craig <james.craig@certara.com>
Repository: CRAN
Date/Publication: 2025-03-03 11:50:24 UTC

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

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

Source

Certara