Files in saezlab/CARNIVAL

A CAusal Reasoning tool for Network Identification (from gene expression data) using Integer VALue programming

.github/ISSUE_TEMPLATE/issue_template.md NEWS.md R/add_perturbation_node.R R/api_run_carnival.R R/check_inputs.R R/check_measurements.R R/check_perturbations.R R/check_prior_knowledge_network.R R/check_solver_param.R R/check_weights.R R/cleanup_carnival.R R/constraints_auxilliary.R R/constraints_create_constraints_1_2_3.R R/constraints_create_constraints_4_5.R R/constraints_create_constraints_6_7.R R/constraints_create_constraints_8.R R/constraints_create_constraints_measurements.R R/constraints_create_loop_constraints.R R/control_node_identifiers.R R/create_lp_formulation.R R/create_objective_function.R R/create_run_metainfo.R R/create_variables.R R/prune_network.R R/set_carnival_options.R R/set_solver_path.R R/solve_carnival.R R/solvers_cbc__solve_cbc.R R/solvers_cplex__parse_cplex_log.R R/solvers_cplex__solve_cplex.R R/solvers_cplex__write_cplex_command_file.R R/solvers_export_results.R R/solvers_gurobi__solve_gurobi.R R/solvers_lpsolve__prepare_lp_matrix_single.R R/solvers_lpsolve__solve_lpsolve.R R/solvers_lpsolve__transform_binaries.R R/solvers_lpsolve__transform_bounds.R R/solvers_lpsolve__transform_constraints.R R/solvers_lpsolve__transform_objective_function.R R/solvers_lpsolve__transform_variables.R R/write_solver_files.R README.Rmd README.md man/addPerturbationNodes.Rd man/checkCarnivalOptions.Rd man/checkData.Rd man/checkOptionsValidity.Rd man/checkPriorKnowledgeNetwork.Rd man/createInternalDataRepresentation.Rd man/defaultCbcSolveCarnivalOptions.Rd man/defaultCplexCarnivalOptions.Rd man/defaultCplexSpecificOptions.Rd man/defaultLpSolveCarnivalOptions.Rd man/generateLpFileCarnival.Rd man/getOptionsList.Rd man/getSupportedSolvers.Rd man/getSupportedSolversFunctions.Rd man/isInputValidCarnival.Rd man/parseCplexLog.Rd man/prepareForCarnivalRun.Rd man/preprocessPriorKnowledgeNetwork.Rd man/processSolution.Rd man/prune_network.Rd man/readOptions.Rd man/runCARNIVAL.Rd man/runFromLpCarnival.Rd man/runInverseCarnival.Rd man/runVanillaCarnival.Rd man/searchForCPLEXSolver.Rd man/sendTaskToSolver.Rd man/setCarnivalOptions.Rd man/solveCarnival.Rd man/solveCarnivalFromLp.Rd man/solveWithCbc.Rd man/solveWithGurobi.Rd man/suggestedCbcSpecificOptions.Rd man/suggestedCplexSpecificOptions.Rd man/testRunCplex.Rd man/writeCplexCommandFileFromJson.Rd man/writeParsedData.Rd parameters/README.md tests/testthat.R tests/testthat/create_dummy_data_n.R tests/testthat/temp_create_dummy_data.R tests/testthat/test-set_solver_path.R tests/testthat/test_carnival_simplest_case.R tests/testthat/test_cbc_small_models.R tests/testthat/test_constraint_1_2.R tests/testthat/test_constraint_3.R tests/testthat/test_constraint_4_5.R tests/testthat/test_constraint_6_7.R tests/testthat/test_constraint_8.R tests/testthat/test_control_node_identifiers.R tests/testthat/test_cplex_small_models.R tests/testthat/test_createEdgesVariables.R tests/testthat/test_createMeasurementsVariables.R tests/testthat/test_createNodesVariables.R tests/testthat/test_gurobi_small_models.R tests/testthat/test_integration.R tests/testthat/test_inverseCarnival.R tests/testthat/test_lpSolve_small_models.R tests/testthat/test_parse_cplex_log.R tests/testthat/test_weights.R tests/testthat/tests_preprocessPriorKnowledgeNetwork.R vignettes/CARNIVAL-vignette.pdf vignettes/CARNIVAL.Rmd