make_Simcyp_inputs_table: Summarize a PBPK model using parameters pulled from...

In shirewoman2/Consultancy: Standardized tools for using R within the Simcyp Consultancy Team

Summarize a PBPK model using parameters pulled from simulations - UNDER CONSTRUCTION

Description

make_Simcyp_inputs_table will make a neatly formatted, organized, human-readable table of the main Simcyp model inputs based on information included in your simulation(s). It was designed for use with writing compound summary pdfs, and, if you supply the references for each parameter, it will include that information in the table.

This function requires you to first run extractExpDetails_mult to get information about your simulations in a format this function can use. To see what will be included in this table and to see the coded names for each of the parameters that will be included in the table, please run something like:

Details <- extractExpDetails_mult()

TableCheck <- annotateDetails(existing_exp_details = Details, compoundID = "substrate", detail_set = "Simcyp inputs")

and the object Details is what you will provide as input for existing_exp_details. The object TableCheck will show you what information will be included and how to refer to each parameter or detail. The values to listed for each parameter in your table will come from the column titled something like "All files have this value for this compound".

Notes:

• This rounds numeric values to the 5th digit.

• There are some parameters that are included in the standard set of outputs from extractExpDetails_mult that we will ignore: the Simulator version, Ki values set to 1e+06 (the default value in the Simulator for, really, no inhibition), Indmax values of 1 (also the default value in the Simulator for no interaction), etc.

Usage

make_Simcyp_inputs_table(
  existing_exp_details,
  sims_to_include = "all",
  compoundID = NA,
  compound = NA,
  references = NA,
  parameters_to_omit = NA,
  parameters_to_add = NA,
  separate_column_for_ADME = TRUE,
  font = "Palatino Linotype",
  fontsize = 11,
  column_widths = NA,
  save_table = NA,
  page_orientation = "portrait"
)

Arguments

existing_exp_details	the output from running extractExpDetails_mult
sims_to_include	optionally specify which simulation files you'd like to include in the annotated output. Acceptable input: "all" to get everything or else a character vector of the sim results files you want. If these are not present in existing_exp_details, they will be ignored.
compoundID	For which compound do you want to summarize the model parameters? Options are "substrate", "primary metabolite 1", "primary metabolite 2", "secondary metabolite", "inhibitor 1", "inhibitor 2", or "inhibitor 1 metabolite".
compound	optionally supply a specific compound name or part of a specific compound name to get all possible compounds that match that and only compounds that match that. Regular expressions are acceptable here, e.g., compound = "midaz|keto" to find any compound with either "midaz" or "keto" in the name. Not case sensitive. If you request only information on a specific compound, we will assume what what you care about is the set of parameters used for that compound and not whether that compound was the substrate or the inhibitor, so we'll ignore anything you supply for compoundID.
references	a data.frame or csv file listing the source of all the parameters used in the model. The columns must include: "Parameter" or "Detail" (either is fine) the specific parameter of interest with the coded name for that parameter. How can you find out the coded name? Run something like this: annotateDetails(existing_exp_details = Details, compoundID = "substrate", detail_set = "Simcyp inputs") and the column "Detail" will list all of the coded names for the parameters that will be included in this table. They must match exactly or the reference will be omitted. "Reference" the reference for that parameter
parameters_to_omit	optionally specify any parameters to omit from the table. For example, maybe you don't want to include that the biliary clearance was set to 0 because that's just not important. To omit that, you'll need the exact, coded name of that parameter, and you can list any parameters to omit as a character vector. How does one obtain the exact, coded name of a parameter? So glad you asked. Please run something like this: annotateDetails(existing_exp_details = Details, compoundID = "substrate", detail_set = "Simcyp inputs") and the column "Detail" will list all of the coded names for the parameters that will be included in this table by default. In our example, you would specify parameters_to_omit = "CLint_biliary_sub"
parameters_to_add	optionally add any parameters that weren't included by default. Acceptable input is a data.frame with the following columns: SimulatorSection the section of the simulator, e.g., "Phys Chem and Blood Binding", "Absorption", "Distribution", "Elimination", "Interaction", "Transport", "Trial Design", or "Population". These must match those options exactly. Detail (also ok to call this column "Parameter") the parameter name Value the value of this parameter Reference the reference for the parameter (optional)
separate_column_for_ADME	In the table, do you want a separate column for ADME headings – "Absoprtion", "Distribution", etc. – or would you like the ADME headings to be included in the "Parameter" column in the table? Default is TRUE for having a separate column.
font	font to use. Default is "Arial" and any fonts available on your machine in either Word or PowerPoint should be acceptable. If you get Times New Roman in your table when you asked for something else, it means that that font isn't available or maybe wasn't spelled the way R is expecting it. For example, "Calibri" works but "Calibri (Body)" doesn't even though the latter is listed in PowerPoint and Word.
fontsize	the numeric font size for the output table. Default is 11 point.
column_widths	optionally specify what the widths of the columns should be with a numeric vector of the widths in inches, e.g., column_widths = c(1, 2, 1, 1)
save_table	optionally save the output table by supplying a file name in quotes here, e.g., "My nicely formatted table.docx". Do not include any slashes, dollar signs, or periods in the file name. If you leave off the file extension, we'll assume you want it to be ".docx". If there is a column titled "File" in your table, we'll add a caption listing which files were included.
page_orientation	set the page orientation for the Word file output to "portrait" (default) or "landscape"

Value

a formatted table

Examples

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shirewoman2/Consultancy documentation built on Feb. 18, 2025, 10 p.m.