This repository contains the code for the following paper: Guiding dose selection of monoclonal antibodies using a new parameter (AFTIR) for characterizing ligand binding systems

Parameter Files

The parameter files are stored in the data directory and are called "ModelF_DRUG.xlsx" where DRUG can be Atezolizumab, Bevacizumab, Pembrolizumab, or Trastuzumab.

Key R Scripts and Rmarkdown files

These are short Tasks in Rmarkdown or R for generating key figures for the manuscript. They are stored in the ModelF folder.

• Task10 - illustrates some simple graphs for how code can be executed
• Task09f - Varying dose and checking AFTIR for each drug
• Task09dV2 - comparison of simple formulation of AFTIR to the full formulation of AFTIR
• Task05e - Varying other parameters and checking AFTIR accuracy for each drug
• Task04 - look at how changing target accumulation affects AFTIR

Key helper files and functions

These contain the key functions that are called by multiple scripts above. They are also located in the ModelF folder.

• AFIRT_calculation.R
  • read.param.file() = read parameter file from Excel
  • lumped.parameters.theory() = calculates AFTIR from theory
  • lumped parameters.simulation() = calculates AFTIR from simulation
  • simulation() - simulates model for one set of parmeters
• ams_graphics_v2.R - Contains some useful graphics functions
• scale.x.log10(), scale.y.log10() - for properly labeling log scaling
• ams_initialize_scrpt.R - To be called at the top of every Rmd file. Initialization code and some useful constants.
• ams_tmdd_helper.R - Could potentially be helpful for doing sensitivity analysis.
• ivsc_4cmtc_shedct.R - ODE for Model F, written to work with RxODE

Graphical Abstract