README.md

In kylebaron/mread.yaml: Model Specification Using 'yaml'

mread.yaml

The package name will probably change with time. For now, experimenting with alternate methods for model specification. I’m trying to leverage existing markup languages (i.e. yaml) to standardize input a bit and make writing the model more powerful and intuitive.

There is a 100% yaml model specification format in the works. For now, trying to refine specification of ODE models as a series of reactions.

Installation

# install.packages("devtools")
devtools::install_github("kylebaron/mread.yaml")

Example

Setup

library(mread.yaml)
library(dplyr)
library(mrgsolve)

Read some input code

examp <- system.file("examples", "two_cmt_model.cpp", package = "mread.yaml")

We are focusing on this new model specification block:

[ reactions ]

- label: absorption from dosing compartment
  species: gut --> cent
  form: ka * gut
- label: elimination from central compartment
  species: cent --> NULL
  form: cl * conc
- label: distribution to peripheral compartment
  species: cent <--> periph
  form: k12 * cent - k21 * periph

In the [ reactions ] block of this simple model we, write the model in reaction / arrow notation as a series of fluxes:

• absorption from the gut to the central compartment (1)
• elimination (2)
• transfer between the central and peripheral compartments (3)

The remaining parts of the model specification file look similar to what we usually see:

[ prob ]
This is a simple pk model; going to demonstrate how we can specify reactions
as fluxes and put them together as reactions.

[ cmt ] gut cent periph

[ param ] ka = 1.2, cl = 1, v1 = 10, v2 = 40, q = 5

[ main ]
double k10 = cl/v1;
double k12 = q/v2;
double k21 = q/v2;

[ ode_assignments ]
double conc = cent/v1;

[ reactions ]
- label: absorption from dosing compartment
  species: gut --> cent
  form: ka * gut
- label: elimination from central compartment
  species: cent --> NULL
  form: cl * conc
- label: distribution to peripheral compartment
  species: cent <--> periph
  form: k12 * cent - k21 * periph

[ table ] capture cp = cent/v1;

[capture] k10

mread.yaml provides a function to read and parse this type of model specification file and return a model object just like mrgsolve::mread().

mod <- mread_rxn(examp, delta = 0.1, end = 48)

Once the model is loaded, it functions just like you had written it using ODEs

mod
. 
. 
. ------------  source: two_cmt_model.cpp  ------------
. 
.   project: /private/var/fol.../T/RtmpajOFlt
.   shared object: two_cmt_model.cpp-so-a5124f1d0622 
. 
.   time:          start: 0 end: 48 delta: 0.1
.                  add: <none>
. 
.   compartments:  gut cent periph [3]
.   parameters:    ka cl v1 v2 q [5]
.   captures:      k10 cp [2]
.   omega:         0x0 
.   sigma:         0x0 
. 
.   solver:        atol: 1e-08 rtol: 1e-08 maxsteps: 20k
. ------------------------------------------------------

mrgsim(mod, ev(amt = 100)) %>% plot

In fact, all mread_rxn() does, is parse the reactions and write that math as ODEs, creating this .cpp file that gets handled but regular old mread()

[ PROB ]
This is a simple pk model; going to demonstrate how we can specify reactions
as fluxes and put them together as reactions.

[ CMT ]
gut cent periph

[ PARAM ]
ka = 1.2, cl = 1, v1 = 10, v2 = 40, q = 5

[ MAIN ]
double k10 = cl/v1;
double k12 = q/v2;
double k21 = q/v2;

[ TABLE ]
capture cp = cent/v1;

[ CAPTURE ]
k10

[ ODE ]
double conc = cent/v1;

double J01 = ka * gut;
double J02 = cl * conc;
double J03 = k12 * cent - k21 * periph;

dxdt_gut    = -J01;
dxdt_cent   =  J01 -J02 -J03;
dxdt_periph =  J03;

//-------------------------------

kylebaron/mread.yaml documentation built on March 24, 2020, 1:23 a.m.