CNORode: ODE add-on to CellNOptR

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ODE add-on to CellNOptR

Author
David Henriques, Thomas Cokelaer
Date of publication
None
Maintainer
David Henriques <davidpcnet@hotmail.com>
License
GPL-2
Version
1.16.0

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