prepareProject: prepareProject
In lptolik/R4Kappa: Kappa simulation Project

Description Usage Arguments Value Author(s)

Creates a infrastructure required to simulate kappa model with various parameter sets and generate correspondent folder infrastructure

prepareProject(project = NA, numSets = 500, pTable, constantfiles = c("main_rnap_def_rule.ka", 
    "main_rnap_init.ka", "main_rnap_param.ka"), templatefiles = c("var_prom_def.ka", 
    "var_prom_init.ka", "var_prom_rule.ka"), paramfile = c("var_prom_param.ka"), 
    k_min = 0.1, k_max = 10, exec.path = "~/kasim3/KaSim", shFile = NA, 
    jobFile = NA, jobCFile = NA, repReg = "_-", type = c("parallel", 
        "concurrent", "both"), writeDir = FALSE)

`project`	name of the project to be created, new folder will be created to contain the project files, if not specified multi_current_date stub will be used.
`numSets`	number of parameter sets to be generated
`pTable`	Parameter ranges data frame. Should contain columns `param` with parameter names, `Min` and `Max` with parameter ranges. Names in `param` column should match names in the content of `paramfile` files.
`constantfiles`	list of file names containing constant part of the model
`templatefiles`	list of template file names to be used to create model
`paramfile`	list of parameter file names
`k_min`	minimum parameter value factor to be used if `pTable==NA`
`k_max`	maximum parameter value factor to be used if `pTable==NA`
`exec.path`	path to kappa language simulator executables in simulation environment
`shFile`	run script template file name
`jobFile`	job management job file template
`jobCFile`	job management job template file for concurrent simulations
`repReg`	regular expression to be replaced with number of parameter set
`type`	type of the project
`writeDir`	if TRUE project directory and its content will be created