search for: stoichiometric

..., I'm trying to use the law of mass action (the details of which aren't really important) to structure a vector of rate equation which will be passed into an ODE function and solved with associated functions from 'deSolve.' Roughly what this entails is scanning through a very large stoichiometric matrix containing integers which map metabolites to reactions and then assembling a series of monomials that describe the rates of the reactions. I'm running into trouble because R does not like doing numerical operations on characters, but I need the rate to be in symbolic form. Below I'v...

...o convert a vector of string objects to a numeric object by initializing the variables with values. I use the function below to scan through a matrix and create mass action flux relationships: makeMassActionFluxes = function(sMatrix) { #Allocate a matrix with identical dimensions as the inputted stoichiometric matrix temp = matrix(nrow = dim(sMatrix)[1], ncol = dim(sMatrix)[2]) velocities = vector(length = dim(sMatrix)[2]) ## This series of 'for' loops scans the stoichiometrix matrix looking for negative integers. ## Once it identifies a negative integer it pulls the row name and exponentiates...