Files in molsysbio/STASNet
Fit and Simulate Model from Perturbation Data
.TEMPLATEgitignore
.gitignore
AUTHORS
COPYING
ChangeLog
DESCRIPTION
INSTALL_INSTRUCTIONS.txt
NAMESPACE
NEWS
R/RcppExports.R
R/compare_models.R
R/create_model.R
R/fitmodel.R
R/generate_model.R
R/helper_functions.R
R/import_export.R
R/model_manipulation.R
R/model_set.R
R/mra_model.R
R/parameters_comparison.R
R/plotHeatmap.R
R/profile_likelihood.R
R/simulation_model.R
R/toy_data_generation.R
R/zzz.R
README
TODO
cleanup
configure
inst/benchmark.R
inst/build_simulated_data.R
inst/fit_script.R
inst/run_modelset.R
inst/unitTest/MIDAS.csv
inst/unitTest/adjacency.tab
inst/unitTest/basal_activity.dat
inst/unitTest/runit.test_model.R
man/MRAmodel.Rd
man/MRAmodelSet.Rd
man/addLayerLinks.Rd
man/addLink.Rd
man/addPLinfos.Rd
man/addVariableParameters.Rd
man/aggregateDirectPaths.Rd
man/cloneModel.Rd
man/compareParameters.Rd
man/computeFitScore.Rd
man/controlFC.Rd
man/createDataSet.Rd
man/createModel.Rd
man/createModelSet.Rd
man/createSimulation.Rd
man/exportModel.Rd
man/extractModelCore.Rd
man/extractSubmodels.Rd
man/extraction.Rd
man/fitmodel.Rd
man/generateToyDesign.Rd
man/generateToyNetwork.Rd
man/generate_infos.Rd
man/getCombinationMatrix.Rd
man/getDirectPaths.Rd
man/getModelError.Rd
man/getParametersNames.Rd
man/getSamples.Rd
man/getSimulation.Rd
man/importModel.Rd
man/initModel.Rd
man/midasFromData.Rd
man/modelGroup.Rd
man/mul_path.Rd
man/niplotPL.Rd
man/plotHeatmap.Rd
man/plotModelAccuracy.Rd
man/plotModelGraph.Rd
man/plotModelParameters.Rd
man/plotModelScores.MRAmodel.Rd
man/plotModelScores.Rd
man/plotModelScores.modelGroup.Rd
man/plotModelSimulation.Rd
man/plotNetworkGraph.Rd
man/plotParameters.Rd
man/plotParameters.modelGroup.Rd
man/plotResiduals.Rd
man/plotSimulation.Rd
man/printParameters.Rd
man/profileLikelihood.Rd
man/readMIDAS.Rd
man/readNetworkAdj.Rd
man/rebuildModel.Rd
man/rebuildModelSet.Rd
man/refit.Rd
man/refitWithFixedParameter.Rd
man/refitWithVariableParameter.Rd
man/selectMinimalModel.Rd
man/setVariableParameters.Rd
man/simulateModel.Rd
man/sub_data_frame.Rd
man/suggestExtension.Rd
man/testModel.Rd
src/Makevars.in
src/RcppExports.cpp
src/fitmodel_in_CPP.cpp
src/fitmodel_in_CPP.hpp
src/generate_response.cpp
src/generate_response.hpp
src/helper_types.cpp
src/helper_types.hpp
src/identifiability.cpp
src/identifiability.hpp
src/levmar-2.5/Axb.c
src/levmar-2.5/Axb_core.c
src/levmar-2.5/LICENSE
src/levmar-2.5/README.txt
src/levmar-2.5/compiler.h
src/levmar-2.5/expfit.c
src/levmar-2.5/levmar.h
src/levmar-2.5/lm.c
src/levmar-2.5/lm.h
src/levmar-2.5/lm_core.c
src/levmar-2.5/lmbc.c
src/levmar-2.5/lmbc_core.c
src/levmar-2.5/lmblec.c
src/levmar-2.5/lmblec_core.c
src/levmar-2.5/lmbleic.c
src/levmar-2.5/lmbleic_core.c
src/levmar-2.5/lmdemo.c
src/levmar-2.5/lmlec.c
src/levmar-2.5/lmlec_core.c
src/levmar-2.5/misc.c
src/levmar-2.5/misc.h
src/levmar-2.5/misc_core.c
src/mathtree.cpp
src/mathtree.hpp
src/model.cpp
src/model.hpp
src/modelset.cpp
src/modelset.hpp
src/modelstructure.cpp
src/modelstructure.hpp
src/modelwrapper.cpp
src/modelwrapper.hpp
src/rref.hpp
src/wrap_matrices.hpp
src/wrappers.cpp
tests/testthat.R
tests/testthat/basal.dat
tests/testthat/bestfit.rds
tests/testthat/data_error.rds
tests/testthat/data_stim_data.rds
tests/testthat/data_unstim_data.rds
tests/testthat/design_inhib_nodes.rds
tests/testthat/design_inhibitor.rds
tests/testthat/design_measured_nodes.rds
tests/testthat/design_stim_nodes.rds
tests/testthat/design_stimuli.rds
tests/testthat/dumb_basal.dat
tests/testthat/header.csv
tests/testthat/model.mra
tests/testthat/ms_bestfit.rds
tests/testthat/ms_data_error.rds
tests/testthat/ms_data_stim_data.rds
tests/testthat/ms_data_unstim_data.rds
tests/testthat/ms_structure_adjacencyMatrix.rds
tests/testthat/ms_structure_names.rds
tests/testthat/network.tab
tests/testthat/rscores.rds
tests/testthat/structure_adjacencyMatrix.rds
tests/testthat/structure_adjacencyMatrix_0.rds
tests/testthat/structure_adjacencyMatrix_1.rds
tests/testthat/structure_names.rds
tests/testthat/structure_names_0.rds
tests/testthat/structure_names_1.rds
tests/testthat/test_STASNet.R
tests/testthat/test_extraction.R
tests/testthat/test_model_no_error_midas.csv
tests/testthat/test_model_no_error_midas_2.csv
tests/testthat/var_model1.mra
tests/testthat/var_model2.mra
vignettes/STASNet_vignette.Rmd
vignettes/STASNet_vignette.html
vignettes/custom.css
