Certara.ModelResults
is an R package and Shiny GUI used to generate, customize, and report model diagnostic plots and tables from NLME or NONMEM runs.
Users are not limited by the GUI however, Certara.ModelResults
will generate the underlying flextable
and xpose
/ggplot2
code (.R
and/or .Rmd
) for you inside the Shiny application, which you can then use to recreate your plot and table objects in R, ensuring reproducibility and traceability of model diagnostics for reporting output.
install.packages("Certara.ModelResults",
repos = c("https://certara.jfrog.io/artifactory/certara-cran-release-public/",
"https://cloud.r-project.org"),
method = "libcurl")
install.packages("Certara.ModelResults",
repos = c("https://certara.jfrog.io/artifactory/certara-cran-release-public/",
"https://cloud.r-project.org"))
Certara.ModelResults
supports both NLME and NONMEM output files. You can use the built in example xpose_data
objects (xpdb_NLME
and xpdb_NONMEM
) in the package to explore functionality. Simply execute the resultsUI()
function from R to launch the Shiny GUI in your web browser.
library(Certara.ModelResults)
# NLME
resultsUI(xpdb = xpdb_NLME)
# NONMEM
resultsUI(xpdb = xpdb_NONMEM)
There are two methods available to initiate resultsUI()
with your model output files:
1.) Specify one or more previously executed model objects (class NlmePmlModel
from Certara.RsNLME
package) to model
argument
library(Certara.ModelResults)
library(Certara.RsNLME)
model <- pkmodel(numCompartments = 2, data = pkData,
ID = "Subject", Time = "Act_Time", A1 = "Amount", CObs = "Conc",
modelName = "TwCpt_IVBolus_FOCE_ELS")
job <- fitmodel(model)
resultsUI(model = model)
2.) Specify one or more xpdb objects (class xpose_data
from xpose
package for NONMEM or Certara.Xpose.NLME
package for NLME) to xpdb
argument
library(Certara.ModelResults)
library(xpose)
xpdb_ex_NONMEM <- xpose_data(runno = "001", dir = "~/NONMEM/One_Cpt_FirstOrder")
resultsUI(xpdb = xpdb_ex_NONMEM)
xpose
and ggplot2
flextable
plotly
…and more!
With Certara.ModelResults
you can create output reports from your tagged model diagnostics inside the Shiny GUI. After tagging various model diagnostic plots or tables, navigate to the REPORT tab and drag one or more tagged diagnostics to the Report Output container.
Does your organization have their own MS Word style template? Use a custom style template with Certara.ModelResults
by overwriting the default style template at the following location C:\Program Files\R\R-4.0.5\library\Certara.ModelResults\extdata\report_template.docx
. Make sure to save your new template with the name report_template.docx
.
Note: The path C:\Program Files\R\R-4.0.5\library\Certara.ModelResults\extdata\report_template.docx
is only valid for a R 4.0.5
installation on Windows. Depending on your operating system and version of R, the path may be different
Learn more about using a style template with Certara.ModelResults
here.
In order to render reports to pdf
, the rmarkdown
package requires a LaTeX
distribution available on the system. You can easily install this in R using the command below:
install.packages('tinytex')
tinytex::install_tinytex()