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