Files in dkaschek/dMod
Dynamic Modeling and Parameter Estimation in ODE Models

.Rbuildignore
.gitignore
BenchmarkModels/Boehm_JProteomeRes2014/.directory
BenchmarkModels/Boehm_JProteomeRes2014/Boehm_JProteomeRes2014.yaml
BenchmarkModels/Boehm_JProteomeRes2014/General_info.xlsx
BenchmarkModels/Boehm_JProteomeRes2014/d2d_plots.png
BenchmarkModels/Boehm_JProteomeRes2014/experimentalCondition_Boehm_JProteomeRes2014.tsv
BenchmarkModels/Boehm_JProteomeRes2014/measurementData_Boehm_JProteomeRes2014.tsv
BenchmarkModels/Boehm_JProteomeRes2014/model_Boehm_JProteomeRes2014.xml
BenchmarkModels/Boehm_JProteomeRes2014/observables_Boehm_JProteomeRes2014.tsv
BenchmarkModels/Boehm_JProteomeRes2014/parameters_Boehm_JProteomeRes2014.tsv
BenchmarkModels/Boehm_JProteomeRes2014/simulatedData_Boehm_JProteomeRes2014.tsv
BenchmarkModels/Boehm_JProteomeRes2014/visualizationSpecification_Boehm_JProteomeRes2014.tsv
BenchmarkModels/Elowitz_Nature2000/Elowitz_Nature2000.yaml
BenchmarkModels/Elowitz_Nature2000/experimentalCondition_Elowitz_Nature2000.tsv
BenchmarkModels/Elowitz_Nature2000/measurementData_Elowitz_Nature2000.tsv
BenchmarkModels/Elowitz_Nature2000/model_Elowitz_Nature2000.xml
BenchmarkModels/Elowitz_Nature2000/observables_Elowitz_Nature2000.tsv
BenchmarkModels/Elowitz_Nature2000/parameters_Elowitz_Nature2000.tsv
BenchmarkModels/Elowitz_Nature2000/simulatedData_Elowitz_Nature2000.tsv
BenchmarkModels/Fujita_SciSignal2010/Fujita_SciSignal2010.yaml
BenchmarkModels/Fujita_SciSignal2010/General_info.xlsx
BenchmarkModels/Fujita_SciSignal2010/d2d_plots.png
BenchmarkModels/Fujita_SciSignal2010/experimentalCondition_Fujita_SciSignal2010.tsv
BenchmarkModels/Fujita_SciSignal2010/measurementData_Fujita_SciSignal2010.tsv
BenchmarkModels/Fujita_SciSignal2010/model_Fujita_SciSignal2010.xml
BenchmarkModels/Fujita_SciSignal2010/observables_Fujita_SciSignal2010.tsv
BenchmarkModels/Fujita_SciSignal2010/parameters_Fujita_SciSignal2010.tsv
BenchmarkModels/Fujita_SciSignal2010/simulatedData_Fujita_SciSignal2010.tsv
BenchmarkModels/Fujita_SciSignal2010/visualizationSpecification_Fujita_SciSignal2010.tsv
BenchmarkModels/Zheng_PNAS2012/General_info.xlsx
BenchmarkModels/Zheng_PNAS2012/Zheng_PNAS2012.yaml
BenchmarkModels/Zheng_PNAS2012/experimentalCondition_Zheng_PNAS2012.tsv
BenchmarkModels/Zheng_PNAS2012/measurementData_Zheng_PNAS2012.tsv
BenchmarkModels/Zheng_PNAS2012/model_Zheng_PNAS2012.xml
BenchmarkModels/Zheng_PNAS2012/model_Zheng_PNAS2012_old.xml
BenchmarkModels/Zheng_PNAS2012/observables_Zheng_PNAS2012.tsv
BenchmarkModels/Zheng_PNAS2012/parameters_Zheng_PNAS2012.tsv
BenchmarkModels/Zheng_PNAS2012/simulatedData_Zheng_PNAS2012.tsv
DESCRIPTION
NAMESPACE
PEtab2dmod_example.Rmd PEtabTests/0001/0001.md
PEtabTests/0001/0001.py
PEtabTests/0001/_0001.yaml
PEtabTests/0001/_0001_solution.yaml
PEtabTests/0001/_conditions.tsv
PEtabTests/0001/_measurements.tsv
PEtabTests/0001/_model.xml
PEtabTests/0001/_observables.tsv
PEtabTests/0001/_parameters.tsv
PEtabTests/0001/_simulations.tsv
PEtabTests/0002/0002.md
PEtabTests/0002/0002.py
PEtabTests/0002/_0002.yaml
PEtabTests/0002/_0002_solution.yaml
PEtabTests/0002/_conditions.tsv
PEtabTests/0002/_measurements.tsv
PEtabTests/0002/_model.xml
PEtabTests/0002/_observables.tsv
PEtabTests/0002/_parameters.tsv
PEtabTests/0002/_simulations.tsv
PEtabTests/0003/0003.md
PEtabTests/0003/0003.py
PEtabTests/0003/_0003.yaml
PEtabTests/0003/_0003_solution.yaml
PEtabTests/0003/_conditions.tsv
PEtabTests/0003/_measurements.tsv
PEtabTests/0003/_model.xml
PEtabTests/0003/_observables.tsv
PEtabTests/0003/_parameters.tsv
PEtabTests/0003/_simulations.tsv
PEtabTests/0004/0004.md
PEtabTests/0004/0004.py
PEtabTests/0004/_0004.yaml
PEtabTests/0004/_0004_solution.yaml
PEtabTests/0004/_conditions.tsv
PEtabTests/0004/_measurements.tsv
PEtabTests/0004/_model.xml
PEtabTests/0004/_observables.tsv
PEtabTests/0004/_parameters.tsv
PEtabTests/0004/_simulations.tsv
PEtabTests/0005/0005.md
PEtabTests/0005/0005.py
PEtabTests/0005/_0005.yaml
PEtabTests/0005/_0005_solution.yaml
PEtabTests/0005/_conditions.tsv
PEtabTests/0005/_measurements.tsv
PEtabTests/0005/_model.xml
PEtabTests/0005/_observables.tsv
PEtabTests/0005/_parameters.tsv
PEtabTests/0005/_simulations.tsv
PEtabTests/0005/conversion_modified.xml
PEtabTests/0006/0006.md
PEtabTests/0006/0006.py
PEtabTests/0006/_0006.yaml
PEtabTests/0006/_0006_solution.yaml
PEtabTests/0006/_conditions.tsv
PEtabTests/0006/_measurements.tsv
PEtabTests/0006/_model.xml
PEtabTests/0006/_observables.tsv
PEtabTests/0006/_parameters.tsv
PEtabTests/0006/_simulations.tsv
PEtabTests/0007/0007.md
PEtabTests/0007/0007.py
PEtabTests/0007/_0007.yaml
PEtabTests/0007/_0007_solution.yaml
PEtabTests/0007/_conditions.tsv
PEtabTests/0007/_measurements.tsv
PEtabTests/0007/_model.xml
PEtabTests/0007/_observables.tsv
PEtabTests/0007/_parameters.tsv
PEtabTests/0007/_simulations.tsv
PEtabTests/0008/0008.md
PEtabTests/0008/0008.py
PEtabTests/0008/_0008.yaml
PEtabTests/0008/_0008_solution.yaml
PEtabTests/0008/_conditions.tsv
PEtabTests/0008/_measurements.tsv
PEtabTests/0008/_model.xml
PEtabTests/0008/_observables.tsv
PEtabTests/0008/_parameters.tsv
PEtabTests/0008/_simulations.tsv
PEtabTests/0009/0009.md
PEtabTests/0009/0009.py
PEtabTests/0009/_0009.yaml
PEtabTests/0009/_0009_solution.yaml
PEtabTests/0009/_conditions.tsv
PEtabTests/0009/_measurements.tsv
PEtabTests/0009/_model.xml
PEtabTests/0009/_observables.tsv
PEtabTests/0009/_parameters.tsv
PEtabTests/0009/_simulations.tsv
PEtabTests/0010/0010.md
PEtabTests/0010/0010.py
PEtabTests/0010/_0010.yaml
PEtabTests/0010/_0010_solution.yaml
PEtabTests/0010/_conditions.tsv
PEtabTests/0010/_measurements.tsv
PEtabTests/0010/_model.xml
PEtabTests/0010/_observables.tsv
PEtabTests/0010/_parameters.tsv
PEtabTests/0010/_simulations.tsv
PEtabTests/0010/conversion_modified.xml
PEtabTests/0011/0011.md
PEtabTests/0011/0011.py
PEtabTests/0011/_0011.yaml
PEtabTests/0011/_0011_solution.yaml
PEtabTests/0011/_conditions.tsv
PEtabTests/0011/_measurements.tsv
PEtabTests/0011/_model.xml
PEtabTests/0011/_observables.tsv
PEtabTests/0011/_parameters.tsv
PEtabTests/0011/_simulations.tsv
PEtabTests/0011/conversion_modified.xml
PEtabTests/0012/0012.md
PEtabTests/0012/0012.py
PEtabTests/0012/_0012.yaml
PEtabTests/0012/_0012_solution.yaml
PEtabTests/0012/_conditions.tsv
PEtabTests/0012/_measurements.tsv
PEtabTests/0012/_model.xml
PEtabTests/0012/_observables.tsv
PEtabTests/0012/_parameters.tsv
PEtabTests/0012/_simulations.tsv
PEtabTests/0013/0013.md
PEtabTests/0013/0013.py
PEtabTests/0013/_0013.yaml
PEtabTests/0013/_0013_solution.yaml
PEtabTests/0013/_conditions.tsv
PEtabTests/0013/_measurements.tsv
PEtabTests/0013/_model.xml
PEtabTests/0013/_observables.tsv
PEtabTests/0013/_parameters.tsv
PEtabTests/0013/_simulations.tsv
PEtabTests/0013/conversion_modified.xml
PEtabTests/0014/0014.md
PEtabTests/0014/0014.py
PEtabTests/0014/_0014.yaml
PEtabTests/0014/_0014_solution.yaml
PEtabTests/0014/_conditions.tsv
PEtabTests/0014/_measurements.tsv
PEtabTests/0014/_model.xml
PEtabTests/0014/_observables.tsv
PEtabTests/0014/_parameters.tsv
PEtabTests/0014/_simulations.tsv
PEtabTests/0015/0015.md
PEtabTests/0015/0015.py
PEtabTests/0015/_0015.yaml
PEtabTests/0015/_0015_solution.yaml
PEtabTests/0015/_conditions.tsv
PEtabTests/0015/_measurements.tsv
PEtabTests/0015/_model.xml
PEtabTests/0015/_observables.tsv
PEtabTests/0015/_parameters.tsv
PEtabTests/0015/_simulations.tsv
PEtabTests/0016/0016.md
PEtabTests/0016/0016.py
PEtabTests/0016/_0016.yaml
PEtabTests/0016/_0016_solution.yaml
PEtabTests/0016/_conditions.tsv
PEtabTests/0016/_measurements.tsv
PEtabTests/0016/_model.xml
PEtabTests/0016/_observables.tsv
PEtabTests/0016/_parameters.tsv
PEtabTests/0016/_simulations.tsv
R/SBMLinterface.R R/classes.R R/dMod.R R/dModFrameClass.R R/data.R R/dataClass.R R/dfoptim.R R/eqnClass.R R/eventClass.R R/nlme.R R/normIndiv.R R/normIndiv_OLD.R R/objClass.R R/odeClass.R R/parClass.R R/parameters.R R/plots.R R/prdClass.R R/prediction.R R/remoteComputing.R R/statistics.R R/steadyStates.R R/strings.R R/symbolics.R R/symmetryDetection.R R/testing.R R/tools.R
R/toolsDaniel.R
R/toolsDenial.R R/toolsMarcus.R R/toolsMirjam.R R/toolsSeverin.R R/toolsSvenja.R R/trust.R R/trustL1.R README.Rmd
README.html
README.md
README_files/figure-html/data-1.png
README_files/figure-html/data-2.png
README_files/figure-html/prediction-1.png
README_files/figure-html/profiles-1.png
README_files/figure-html/trust-1.png
dMod.Rproj
data/BAdata.tab
data/jakstat.tab
inst/CITATION
inst/code/AlyssaPetit_ver1.0.py
inst/code/AlyssaPetit_ver1.1.py
inst/code/buildSystem.py
inst/code/checkPredictions.py
inst/code/extendObservation.py
inst/code/functions.py
inst/code/functions_obs.py
inst/code/polyClass.py
inst/code/quasiSteadyStates.py
inst/code/readData.py
inst/code/sbmlAmiciDmod.py
inst/code/symmetryDetection.py
inst/examples/PKPD.R inst/examples/dMod.frame.R inst/examples/dMod_example_ABC_2cond.R
inst/examples/dModtoShiny/CCD4/ccd4.so
inst/examples/dModtoShiny/CCD4/ccd4_s.so
inst/examples/dModtoShiny/CCD4/input_shiny.RData
inst/examples/dModtoShiny/CCD4/obsA.so
inst/examples/dModtoShiny/CCD4/obsA_deriv.so
inst/examples/dModtoShiny/app.R inst/examples/dModtoShiny/input_shiny.R inst/examples/datalist.R inst/examples/define.R inst/examples/eqnlist.R inst/examples/eqnvec.R inst/examples/equations.R inst/examples/errmodel.R inst/examples/events.R inst/examples/example_CCD4/analysis.R
inst/examples/example_CCD4/data_mark_out.csv
inst/examples/example_CCD4/datalist.Rds
inst/examples/example_CCD4/model.csv
inst/examples/example_CCD4/mstrust_CCD4.Rds
inst/examples/example_CCD4/profiles.Rds
inst/examples/example_CCD4/setup.R inst/examples/example_phytoene/analysis.R
inst/examples/example_phytoene/bestfit_pub.Rds
inst/examples/example_phytoene/data_sigma.Rds
inst/examples/example_phytoene/data_triplicates.Rds
inst/examples/example_phytoene/datafile_err_sp_badn.csv
inst/examples/example_phytoene/datafile_err_sp_badn_name.csv
inst/examples/example_phytoene/phyto_simple_pfc_nopfc.csv
inst/examples/example_phytoene/phyto_simple_pfcoop.csv
inst/examples/example_phytoene/setup.R inst/examples/getSteps.R inst/examples/normL2.R inst/examples/objective.R inst/examples/odemodel.R inst/examples/parlist.R inst/examples/parvec.R inst/examples/plotting.R inst/examples/prediction.R inst/examples/profiles.R inst/examples/saveShiny_dMod.frame.R inst/examples/steadystates.R inst/examples/sumdatalist.R inst/examples/test_LOQ.R inst/examples/test_blocks.R inst/templates/R2CTemplate.R inst/templates/R2CTemplateIE.R inst/templates/unitTestTemplate.R inst/testing/AlgebraicFunctions/example1.R inst/testing/EventsAndReducedSensitivities.R inst/testing/JakStat/jakstat.R inst/testing/JakStat/jakstat2.R inst/testing/JakStat/jakstat3.R
inst/testing/JakStat/pnas_data_original.csv
inst/testing/JakStat/topology.csv
inst/testing/JakStat/topology_inputModel.csv
inst/tests/etc/exampleParser-1-Expectation.R inst/tests/etc/exampleParser-1-Input.R inst/tests/etc/exampleParser-2-Expectation.R inst/tests/etc/exampleParser-2-Input.R inst/tests/etc/example_CCD4/001-setup.R inst/tests/etc/example_CCD4/002-writeExpectations.R
inst/tests/etc/example_CCD4/expectations/001-objResult.rds
inst/tests/etc/example_CCD4/expectations/011-data.rds
inst/tests/etc/example_CCD4/expectations/012-resResult.rds
inst/tests/etc/example_CCD4/expectations/013-wrss.rds
inst/tests/etc/example_CCD4/expectations/021-data.rds
inst/tests/etc/example_CCD4/expectations/022-resResultErrpars.rds
inst/tests/etc/example_CCD4/expectations/023-wrss.rds
inst/tests/etc/example_CCD4/expectations/031-data.rds
inst/tests/etc/example_CCD4/expectations/032-resResultErrpars.rds
inst/tests/etc/example_CCD4/expectations/033-wrss.rds
inst/tests/etc/example_CCD4/expectations/041-data.rds
inst/tests/etc/example_CCD4/expectations/042-resResultErrpars.rds
inst/tests/etc/example_CCD4/expectations/043-wrss.rds
inst/tests/etc/example_CCD4/expectations/051-data.rds
inst/tests/etc/example_CCD4/expectations/052-resResultErrpars.rds
inst/tests/etc/example_CCD4/expectations/053-wrss.rds
inst/tests/etc/example_CCD4/expectations/061-data.rds
inst/tests/etc/example_CCD4/expectations/062-resResultErrpars.rds
inst/tests/etc/example_CCD4/expectations/063-wrss.rds
inst/tests/test-bloq.R inst/tests/test-exmpextr.R inst/tests/test-funC0.R inst/tests/test-modelnames.R inst/tests/test-nll_wrss_normIndiv.R inst/tests/test-obj_chisquare.R inst/tests/test-objective.R inst/tests/test-odemodel.R inst/tests/test-plotting.R inst/tests/test-steadystates.R inst/tests/test-sumdatalist.R man/Id.Rd man/P.Rd man/PRD_indiv.Rd man/P_indiv.Rd man/Pexpl.Rd man/Pimpl.Rd man/Xd.Rd man/Xf.Rd man/Xs.Rd man/Xt.Rd man/Y.Rd man/addReaction.Rd man/appendObj.Rd man/appendParframes.Rd man/as.data.frame.dMod.Rd man/as.data.frame.eqnlist.Rd man/as.eqnvec.Rd man/as.eventlist.Rd man/as.objlist.Rd man/as.parframe.Rd man/as.parvec.parframe.Rd man/attrs.Rd man/blockdiagSymb.Rd man/check_and_sanitize_prediction.Rd man/checkout_hypothesis.Rd man/combine.Rd man/compare.Rd man/compile.Rd man/confint.parframe.Rd man/conservedQuantities.Rd man/constraintExp2.Rd man/constraintL2.Rd man/controls.Rd man/coordTransform.Rd man/covariates.Rd man/createExample.Rd man/dMod.frame.Rd man/datalist.Rd man/datapointL2.Rd man/datapointL2_indiv.Rd man/define.Rd man/detectFreeCores.Rd man/distributed_computing.Rd man/dot.Rd man/eqnlist.Rd man/eqnvec.Rd man/eventlist.Rd man/exmpextr.Rd man/expand.grid.alt.Rd man/extractExamples.Rd man/fitErrorModel.Rd man/forcingsSymb.Rd man/format.eqnvec.Rd man/funC0.Rd man/getCoefficients.Rd man/getConditions.Rd man/getDerivs.Rd man/getElements.Rd man/getEquations.Rd man/getEstGridParameterMapping.Rd man/getFluxes.Rd man/getLocalDLLs.Rd man/getObservables.Rd man/getParGrids.Rd man/getParameters.Rd man/getParameters.data.table.Rd man/getParametersToEstimate.Rd man/getReactions.Rd man/getStepIndices.Rd man/getSteps.Rd man/ggopen.Rd man/grapes-.-times-grapes.Rd man/gridlist.Rd man/import_sbml.Rd man/indiv_addGlobalParsToGridlist.Rd man/indiv_addLocalParsToGridList.Rd man/init_empty_objlist.Rd man/jakstat.Rd man/lbind.Rd man/load.parlist.Rd man/loadDLL.Rd man/long2wide.Rd man/lsdMod.Rd man/make_pars.Rd man/match.fnargs.Rd man/mname.Rd man/modelname.Rd man/msParframe.Rd man/mstrust.Rd man/mutatedMod.frame.Rd man/nll.Rd man/nll_ALOQ.Rd man/nll_BLOQ.Rd man/normL2.Rd man/normL2_indiv.Rd man/nullZ.Rd man/objframe.Rd man/objlist.Rd man/objtimes.Rd man/obsfn.Rd man/odemodel.Rd man/optionsLSODES.Rd man/parfn.Rd man/parframe.Rd man/parlist.Rd man/parvec.Rd man/plot.datalist.Rd man/plot.parlist.Rd man/plotArray.Rd man/plotCombined.Rd man/plotData.Rd man/plotFluxes.Rd man/plotPars.Rd man/plotPaths.Rd man/plotPathsMulti.Rd man/plotPrediction.Rd man/plotProfile.Rd man/plotProfilesAndPaths.Rd man/plotResiduals.Rd man/plotValues.Rd man/plus-.datalist.Rd man/plus-.fn.Rd man/plus-.objfn.Rd man/plus-.objlist.Rd man/prdfn.Rd man/prdframe.Rd man/prdlist.Rd man/predict.prdfn.Rd man/predtimes.Rd man/print.eqnlist.Rd man/print.eqnvec.Rd man/print.parfn.Rd man/print.parvec.Rd man/print0.Rd man/priorL2.Rd man/profile.Rd man/profile_pars_per_node.Rd man/progressBar.Rd man/python_version_request.Rd man/python_version_rpython.Rd man/python_version_sys.Rd man/reduceReplicates.Rd man/renameDerivPars.Rd man/renameDerivParsInObjlist.Rd man/repWithNames.Rd man/repar.Rd man/res.Rd man/resolveRecurrence.Rd man/rref.Rd man/runbg.Rd man/runbgInstall.Rd man/runbg_bwfor.Rd man/runbg_bwfor_slurm.Rd man/runbg_bwfor_sshpass.Rd man/saveShiny.Rd man/saveShiny_dMod.frame.Rd man/scale_color_dMod.Rd man/scale_fill_dMod.Rd man/stat.parlist.Rd man/steadyStates.Rd man/strelide.Rd man/strpad.Rd man/submatrix.Rd man/subset.eqnlist.Rd man/sumDuplicatedParsInDeriv.Rd man/sumDuplicatedParsInObjlist.Rd man/summary.eqnvec.Rd man/symmetryDetection.Rd man/theme_dMod.Rd man/timepointL2_indiv.Rd man/times-.fn.Rd man/trust.Rd man/unique.parframe.Rd man/vcov.Rd man/wide2long.Rd man/wide2long.data.frame.Rd man/wide2long.list.Rd man/wide2long.matrix.Rd man/write.eqnlist.Rd
todo.txt
vignettes/BA_publication.R vignettes/BA_publication_part1.R vignettes/BA_publication_part2.R vignettes/BA_publication_part3.R vignettes/BA_transport_model.R vignettes/BA_workshop.Rmd vignettes/NLME.R vignettes/NLME_example2.R vignettes/PKmodel.R vignettes/Pimpl_Pexpl.Rmd
vignettes/ba_chart.png
vignettes/bloq.rmd vignettes/concatenation.Rmd vignettes/dMod.R vignettes/dMod.Rmd
vignettes/dMod.html
vignettes/dmodtoshiny.png
vignettes/event_estimation.Rmd vignettes/getFunctions.Rmd vignettes/lists.Rmd
vignettes/pathway.png
vignettes/shinyapp.Rmd vignettes/solvers.Rmd
vignettes/topology.csv
dkaschek/dMod documentation built on July 27, 2023, 11:45 p.m.