system_new: Create New 'system.txt' File

In john-harrold/ubiquity: PKPD, PBPK, and Systems Pharmacology Modeling Tools

Create New system.txt File

Description

Copy a blank template (system_file="template") file to the working directory or an example by specifying the following:

• "template" - Empty system file template

• "adapt" - Parent/metabolite model taken from the adapt manual used in estimation examples [ADAPT]

• "two_cmt_cl" - Two compartment model parameterized in terms of clearances

• "one_cmt_cl" - One compartment model parameterized in terms of clearances

• "two_cmt_micro" - Two compartment model parameterized in terms of rates (micro constants)

• "one_cmt_micro" - One compartment model parameterized in terms of rates (micro constants)

• "mab_pk" - General compartmental model of mAb PK from Davda 2014 [DG]

• "pbpk" - PBPK model of mAb disposition in mice from Shah 2012 [SB]

• "pbpk_template" - System parameters from Shah 2012 [SB] have been defined for all species along with the set notation to be used as a template for developing models with physiological parameters

• "pwc" - Example showing how to make if/then or piece-wise continuous variables

• "tmdd" - Model of antibody with target-mediated drug disposition

• "tumor" - Transit tumor growth model taken from Lobo 2002 [LB]

Usage

system_new(
  file_name = "system.txt",
  system_file = "template",
  overwrite = FALSE,
  output_directory = getwd()
)

Arguments

file_name	name of the new file to create
system_file	name of the system file to copy
overwrite	if TRUE the new system file will overwrite any existing files present
output_directory	getwd() directory where system file will be placed

Details

References

• [ADAPT] Adapt 5 Users Guide https://bmsr.usc.edu/files/2013/02/ADAPT5-User-Guide.pdf

• [DG] Davda et. al. mAbs (2014) 6(4):1094-1102 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.4161/mabs.29095")}

• [LB] Lobo, E.D. & Balthasar, J.P. AAPS J (2002) 4, 212-222 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1208/ps040442")}

• [SB] Shah, D.K. & Betts, A.M. JPKPD (2012) 39 (1), 67-86 \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/s10928-011-9232-2")}

Value

TRUE if the new file was created and FALSE otherwise

Examples

# To create an example system file named example_system.txt:
system_new(system_file      = "mab_pk", 
           file_name        = "system_example.txt", 
           overwrite        = TRUE,  
           output_directory = tempdir())

john-harrold/ubiquity documentation built on June 11, 2025, 1:34 a.m.