tidy_input_PK: Tidy input PK data as needed

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

Tidy input PK data as needed

Description

INTERNAL PACKAGE USE ONLY. Reads (as needed), harmonizes and tidies observed PK input. Output is a data.frame of PK parameters with columns File, Sheet, CompoundID, Tissue, Value, and Variability. The columns Sheet, Value, and Variability may contain NAs.

Usage

tidy_input_PK(
  PKparameters,
  sim_data_files = NA,
  existing_exp_details = NA,
  compoundsToExtract = "substrate",
  tissues = "plasma",
  sheet_PKparameters = NA
)

Arguments

PKparameters	whatever they have supplied for PKparameters for pksummary_table or pksummary_mult. This can be a csv file, a character vector, or NA.
sim_data_files	a character vector of file names. This should no longer be NA or "recursive".
existing_exp_details	If you have already run extractExpDetails_mult to get all the details from the "Input Sheet" (e.g., when you ran extractExpDetails you said exp_details = "Summary and Input" or exp_details = "all"), you can save some processing time by supplying that object here, unquoted. If left as NA, this function will run extractExpDetails behind the scenes anyway to figure out some information about your experimental set up.
compoundsToExtract	the values they supplied for compoundsToExtract in the parent function.
tissues	the values they supplied for tissues in the parent function
sheet_PKparameters	the values they supplied for sheet_PKparameters in the parent function
report_input_file	probably not in use
sheet_report	probably not in use

Value

a list of: 1) "PKparameters" – a tidy data.frame of PKparameters with standardized column names and contents, 2) "existing_exp_details", which will only differ from the original in that any missing sim files will be added – none will be removed. 3) "FilePairs" – if this is from calc_PK_ratios, then a tidy data.frame listing which items should be paired

Examples

# nope 

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