template_spec_reac: produce i01 file

Description Usage Arguments Value

View source: R/template_spec_reac.R

Description

produce the template for species and reactions read the reaction file formated as template/addon.reac.tab

Usage

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template_spec_reac(path = NULL, type = "mm", dir.data = NULL,
  modified.file = "", para.list = NULL, list.exi = NULL,
  extend = 1, rand = FALSE, rand.seed = 0)

Arguments

path

string. the reaction file path. must be provided

type

string. the reaction type that need to be formated "mr": mass reaction "mm": Michaelis–Menten kinetics. default

dir.data

string. the data directory(working folder). must be provided

modified.file

string. the addon name. default ""

para.list

list. the input parameter list that need to be changed a list contains parameters related to species and reactions. must be provided

Attention: if there is no regulation to formualte then regu=NULL species: obsv(jmsspec), fixed(jctspec), initial(4th, 5th of ivpm) const(jfix) react: kine(kinetic parameter list), enz(the enzyme in mm reaction, need for ranking), rev(reversible, 1 indicate reversible 0 non-reversible),

list.exi

list. existing species and reactions list. default NULL

extend

numeric the enlarge amount/by proportion of parameters(k1 k2). default 1

rand

bool. related to generating initial theta. FALSE not randomeness, geometry mean of the boundary. TRUE unif random generating. default FALSE

rand.seed

numeric. the seed for sampling initial condiiton. default 0

Value

list. parameters and related sizes


artedison/ensRadaptor documentation built on Dec. 8, 2020, 5:31 p.m.