CNORode: ODE add-on to CellNOptR

ODE add-on to CellNOptR

AuthorDavid Henriques, Thomas Cokelaer
Date of publicationNone
MaintainerDavid Henriques <davidpcnet@hotmail.com>
LicenseGPL-2
Version1.16.0

View on Bioconductor

Man pages

cnolistCNORodeExample: A cnolist from CellNoptR

CNORode-package: Logic based ODE extension for CellNOptR

createLBodeContPars: Create a list with ODE parameter information needed to...

defaultParametersGA: Create default options to perform parameter estimation with a...

defaultParametersSSm: Create default options to perform parameter estimation with...

getLBodeContObjFunction: Returns the objective function to perform parameter...

getLBodeDataSim: Simulate value signals a CNO list With Logic-Based ODEs.

getLBodeMINLPObjFunction: Get the objective function to evaluate the fitness of a given...

getLBodeModelSim: Simulate the logic-based ODE model

getLBodeSimFunction: Get a function to simulate a logic based ODE model.

getStates: Find which species in the model are states.

incidence2Adjacency: Convert an incidence matrix into an adjacency matrix.

indices: Indices that relate cnolist to model

minlpLBodeSSm: Search for the best combination of continuous parameters and...

model: A model from CellNoptR

parEstimationLBode: Perform parameter estimation using a genetic algorithm...

parEstimationLBodeGA: Perform parameter estimation using a genetic algorithm...

parEstimationLBodeSSm: Perform parameter estimation using essR.

plotLBodeFitness: Plot data against simulated values.

plotLBodeModelSim: Simulate the model and plot the obtained with the different...

simdata2cnolist: converts output of getLBodeModelSim to cnolist

simulate: Simulate value signals a CNO list With Logic-Based ODEs.

Files in this package

CNORode/DESCRIPTION
CNORode/NAMESPACE
CNORode/R
CNORode/R/createLBodeContPars.R CNORode/R/defaultParametersGA.R CNORode/R/defaultParametersSSm.R CNORode/R/getLBodeContObjFunction.R CNORode/R/getLBodeDataSim.R CNORode/R/getLBodeMINLPObjFunction.R CNORode/R/getLBodeModelSim.R CNORode/R/getLBodeSimFunction.R CNORode/R/getStates.R CNORode/R/incidence2Adjacency.R CNORode/R/minlpLBodeSSm.R CNORode/R/parEstimationLBode.R CNORode/R/parEstimationLBodeGA.R CNORode/R/parEstimationLBodeSSm.R CNORode/R/plotLBodeFitness.R CNORode/R/plotLBodeModelSim.R CNORode/R/simdata2cnolist.R CNORode/R/simulate.R CNORode/R/zzz.R
CNORode/build
CNORode/build/vignette.rds
CNORode/data
CNORode/data/ToyCNOlist.RData
CNORode/data/ToyIndices.RData
CNORode/data/ToyModel.RData
CNORode/inst
CNORode/inst/NEWS.Rd
CNORode/inst/doc
CNORode/inst/doc/CNORode-vignette.R
CNORode/inst/doc/CNORode-vignette.Rnw
CNORode/inst/doc/CNORode-vignette.pdf
CNORode/inst/doc/ToyModelMMB_FeedbackAnd.csv
CNORode/inst/doc/ToyModelMMB_FeedbackAnd.sif
CNORode/man
CNORode/man/CNORode-package.Rd CNORode/man/cnolistCNORodeExample.Rd CNORode/man/createLBodeContPars.Rd CNORode/man/defaultParametersGA.Rd CNORode/man/defaultParametersSSm.Rd CNORode/man/getLBodeContObjFunction.Rd CNORode/man/getLBodeDataSim.Rd CNORode/man/getLBodeMINLPObjFunction.Rd CNORode/man/getLBodeModelSim.Rd CNORode/man/getLBodeSimFunction.Rd CNORode/man/getStates.Rd CNORode/man/incidence2Adjacency.Rd CNORode/man/indices.Rd CNORode/man/minlpLBodeSSm.Rd CNORode/man/model.Rd CNORode/man/parEstimationLBode.Rd CNORode/man/parEstimationLBodeGA.Rd CNORode/man/parEstimationLBodeSSm.Rd CNORode/man/plotLBodeFitness.Rd CNORode/man/plotLBodeModelSim.Rd CNORode/man/simdata2cnolist.Rd CNORode/man/simulate.Rd
CNORode/src
CNORode/src/CNOStructure.h
CNORode/src/Makevars
CNORode/src/Toy_Model_MMB_Feedback_OriginalPars_C_test.h
CNORode/src/cvodea.c
CNORode/src/cvodea_io.c
CNORode/src/cvodes.c
CNORode/src/cvodes_band.c
CNORode/src/cvodes_bandpre.c
CNORode/src/cvodes_bandpre_impl.h
CNORode/src/cvodes_bbdpre.c
CNORode/src/cvodes_bbdpre_impl.h
CNORode/src/cvodes_dense.c
CNORode/src/cvodes_diag.c
CNORode/src/cvodes_diag_impl.h
CNORode/src/cvodes_direct.c
CNORode/src/cvodes_direct_impl.h
CNORode/src/cvodes_impl.h
CNORode/src/cvodes_io.c
CNORode/src/cvodes_spbcgs.c
CNORode/src/cvodes_spgmr.c
CNORode/src/cvodes_spils.c
CNORode/src/cvodes_spils_impl.h
CNORode/src/cvodes_sptfqmr.c
CNORode/src/decimal2binary.c
CNORode/src/findStates.c
CNORode/src/fnvector_serial.c
CNORode/src/fnvector_serial.h
CNORode/src/getAdjacencyMatrix.c
CNORode/src/getNumBits.c
CNORode/src/getNumInputs.c
CNORode/src/getStateIndex.c
CNORode/src/getTruthTables.c
CNORode/src/get_count_bits.c
CNORode/src/get_input_index.c
CNORode/src/get_support_truth_tables.c
CNORode/src/get_truth_tables_index.c
CNORode/src/hill_function.c
CNORode/src/include
CNORode/src/include/cvodes
CNORode/src/include/cvodes/cvodes.h
CNORode/src/include/cvodes/cvodes_band.h
CNORode/src/include/cvodes/cvodes_bandpre.h
CNORode/src/include/cvodes/cvodes_bbdpre.h
CNORode/src/include/cvodes/cvodes_dense.h
CNORode/src/include/cvodes/cvodes_diag.h
CNORode/src/include/cvodes/cvodes_direct.h
CNORode/src/include/cvodes/cvodes_lapack.h
CNORode/src/include/cvodes/cvodes_spbcgs.h
CNORode/src/include/cvodes/cvodes_spgmr.h
CNORode/src/include/cvodes/cvodes_spils.h
CNORode/src/include/cvodes/cvodes_sptfqmr.h
CNORode/src/include/nvector
CNORode/src/include/nvector/nvector_serial.h
CNORode/src/include/sundials
CNORode/src/include/sundials/sundials_band.h
CNORode/src/include/sundials/sundials_config.h
CNORode/src/include/sundials/sundials_dense.h
CNORode/src/include/sundials/sundials_direct.h
CNORode/src/include/sundials/sundials_fnvector.h
CNORode/src/include/sundials/sundials_iterative.h
CNORode/src/include/sundials/sundials_lapack.h
CNORode/src/include/sundials/sundials_math.h
CNORode/src/include/sundials/sundials_nvector.h
CNORode/src/include/sundials/sundials_spbcgs.h
CNORode/src/include/sundials/sundials_spgmr.h
CNORode/src/include/sundials/sundials_sptfqmr.h
CNORode/src/include/sundials/sundials_types.h
CNORode/src/linear_transfer_function.c
CNORode/src/normHill.c
CNORode/src/nvector_serial.c
CNORode/src/printAdjMat.c
CNORode/src/printInterMat.c
CNORode/src/printNminiTerms.c
CNORode/src/printTruthTables.c
CNORode/src/rhsODE.c
CNORode/src/sim_logic_ode.c
CNORode/src/simulateODE.c
CNORode/src/sundials_band.c
CNORode/src/sundials_dense.c
CNORode/src/sundials_direct.c
CNORode/src/sundials_iterative.c
CNORode/src/sundials_math.c
CNORode/src/sundials_nvector.c
CNORode/src/sundials_spbcgs.c
CNORode/src/sundials_spgmr.c
CNORode/src/sundials_sptfqmr.c
CNORode/vignettes
CNORode/vignettes/CNORode-vignette.Rnw
CNORode/vignettes/ToyModelMMB_FeedbackAnd.png
CNORode/vignettes/ToyModelMMB_FeedbackAnd.svg
CNORode/vignettes/comp_tex.bat
CNORode/vignettes/data_ToyModelMMB_FeddbackAnd.pdf

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