prepareProject: prepareProject

Description Usage Arguments Value Author(s)

View source: R/prepareProject.R

Description

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

Usage

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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)

Arguments

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

Value

project object

Author(s)

Anatoly Sorokin


lptolik/R4Kappa documentation built on May 21, 2017, 2:42 p.m.