DA.cat: Estimation of single catalytic constant using the diffusion...

In SIfEK: Statistical Inference for Enzyme Kinetics

Description

The function estimates single catalytic constant using single data set with an initial enzyme concentrations and substrate concentration. The diffusion approximation is utilized for the likelihood function.

Usage

DA.cat(method = T, dat, enz, subs, MM, catal, nrepeat = 10000,
  jump = 1, burning = 0, catal_m_v = c(1, 10000), sig,
  scale_tun = 80)

Arguments

method	method selection: T=TQ model, F=SQ model(default = T)
dat	observed dataset ( time & trajectory columns)
enz	enzyme concentration
subs	substrate concentration
MM	true value of MM constant
catal	initial value of catalytic constant
nrepeat	total number of iteration (default=10000)
jump	length of distance (default =1)
burning	lenth of burning period (default =0)
catal_m_v	Catalytic prior gamma mean, variance(default=c(1,10000))
sig	standard deviation of univariate Normal proposal distribution
scale_tun	scale tunning constant for stochastic simulation

Details

The function DA.cat generates a set of MCMC simulation samples from the conditional posterior distribution of catalytic constant of enzyme kinetics model. As the catalytic constant is only parameter to be estimated in the function the user should assign MM constant as well as initial enzyme concentration and substrate concentration. The prior information for the parameter can be given. The turning constant (scale_tun) and standard deviation (sig) can be set to controlled proper mixing and acceptance ratio of the parameter from the conditional posterior distribution. The posterior samples are only stored with fixed interval according to set "jump" to reduce serial correlation. The initial iterations are removed for convergence. The “burning” is set the length of initial iterations. The diffusion approximation method is used for construction of the likelihood.

Value

A vector of posterior samples of catalytic constant

Examples

## Not run: 
data('Chymo_low')
sk_DA=DA.cat(method=TRUE,dat=Chymo_low,enz=4.4e+7,subs = 4.4e+7,MM=4.4e+8,catal=0.05
                  ,nrepeat=10000,jump=1,burning = 0,catal_m_v=c(1,10000),sig=0.005)

## End(Not run)

SIfEK documentation built on May 1, 2019, 9:11 p.m.