Description Usage Arguments Value
View source: R/template_spec_reac.R
produce the template for species and reactions read the reaction file formated as template/addon.reac.tab
1 2 3 |
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 |
list. parameters and related sizes
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