Files in jpahle/CoRC
COPASI R Connector

.Rbuildignore
.gitignore
.gitmodules
CoRC.Rproj
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/CoRC.R R/entity_accessors.R R/entity_finders.R R/model_building.R R/model_management.R R/model_properties.R R/roxygen_helpers.R
R/swig_wrapper.R
R/task_lna.R R/task_mca.R R/task_optimization.R R/task_parameterestimation.R R/task_sigmapoint.R R/task_steadystate.R R/task_timecourse.R R/utils.R R/utils_copasi_vector.R R/utils_expressions.R R/utils_keys.R R/utils_parallel.R R/utils_stringr.R R/utils_swig.R R/utils_tasks.R README.Rmd README.md
_pkgdown.yml
development/auto_tester/README
development/auto_tester/container_copasi_dev/Dockerfile
development/auto_tester/container_copasi_release/Dockerfile
development/auto_tester/container_r_devel/Dockerfile
development/auto_tester/container_r_var/Dockerfile
development/auto_tester/container_r_var/full_test.sh
development/auto_tester/test_copasi_dev_biomodels.sh
development/auto_tester/test_copasi_dev_pkg.sh
development/auto_tester/test_copasi_release_biomodels.sh
development/auto_tester/test_copasi_release_pkg.sh
development/auto_tester/test_lib_with_r_var.sh
development/auto_tester/test_master_with_r_devel.sh
development/compile_copasi.Rmd
development/copasi-source/CopasiVersion.h
development/copasi-source/build_darwin_x64_clean.sh
development/copasi-source/build_darwin_x64_quick.sh
development/copasi-source/build_linux_x64_clean.sh
development/copasi-source/build_linux_x64_quick.sh
development/copasi-source/build_windows_x64_clean.bat
development/copasi-source/build_windows_x64_quick.bat
development/copasi-source/compilers/linux_x64/Dockerfile
development/copasi-source/compilers/windows_x64/Dockerfile
development/copasi-source/compilers/windows_x64/entrypoint.bat
development/copasi-source/compilers/windows_x64/r_lib_extractor/README
development/copasi-source/compilers/windows_x64/r_lib_extractor/README.txt
development/copasi-source/compilers/windows_x64/r_lib_extractor/expdef64.exe
development/copasi-source/d_build_linux_x64_clean.ps1
development/copasi-source/d_build_linux_x64_clean.sh
development/copasi-source/d_build_linux_x64_quick.ps1
development/copasi-source/d_build_linux_x64_quick.sh
development/copasi-source/d_build_windows_x64_clean.ps1
development/copasi-source/d_build_windows_x64_clean.sh
development/copasi-source/d_build_windows_x64_quick.ps1
development/copasi-source/d_build_windows_x64_quick.sh
development/dev_documentation.Rmd development/dev_setup.Rmd development/dev_tools.R development/patch-swig-wrapper.R development/site_upgrade.R development/update-swig-in-package.R
docs/LICENSE-text.html
docs/articles/CoRC.html
docs/articles/CoRC_files/figure-html/unnamed-chunk-9-1.png
docs/articles/entity_management.html
docs/articles/examples.html
docs/articles/examples_files/crosstalk-1.0.0/css/crosstalk.css
docs/articles/examples_files/crosstalk-1.0.0/js/crosstalk.js
docs/articles/examples_files/crosstalk-1.0.0/js/crosstalk.js.map
docs/articles/examples_files/crosstalk-1.0.0/js/crosstalk.min.js
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docs/articles/examples_files/htmlwidgets-1.2/htmlwidgets.js
docs/articles/examples_files/jquery-1.11.3/jquery-AUTHORS.txt
docs/articles/examples_files/jquery-1.11.3/jquery.js
docs/articles/examples_files/jquery-1.11.3/jquery.min.js
docs/articles/examples_files/jquery-1.11.3/jquery.min.map
docs/articles/examples_files/plotly-binding-4.8.0/lib/colourpicker/LICENSE
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docs/articles/examples_files/plotly-binding-4.8.0/lib/plotlyjs/plotly-htmlwidgets.css
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docs/articles/examples_files/plotly-binding-4.8.0/lib/selectize/selectize.bootstrap3.css
docs/articles/examples_files/plotly-binding-4.8.0/lib/selectize/selectize.min.js
docs/articles/examples_files/plotly-binding-4.8.0/lib/typedarray/LICENSE
docs/articles/examples_files/plotly-binding-4.8.0/lib/typedarray/typedarray.min.js
docs/articles/examples_files/plotly-binding-4.8.0/plotly.js
docs/articles/examples_files/plotly-binding-4.8.0/plotly.yaml
docs/articles/examples_files/plotly-htmlwidgets-css-1.39.2/plotly-htmlwidgets.css
docs/articles/examples_files/plotly-main-1.39.2/plotly-latest.min.js
docs/articles/examples_files/typedarray-0.1/typedarray.min.js
docs/articles/index.html
docs/articles/issues.html
docs/articles/model_building.html
docs/articles/model_building_files/figure-html/unnamed-chunk-3-1.png
docs/articles/model_building_files/figure-html/unnamed-chunk-4-1.png
docs/articles/task_management.html
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/docsearch.json
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/man/figures/logo.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/CoRC-package.html
docs/reference/addExperiments.html
docs/reference/addOptimizationParameter.html
docs/reference/addParameterEstimationParameter.html
docs/reference/applyInitialState.html
docs/reference/autoplot.copasi_ts.html
docs/reference/clearCustomKineticFunctions.html
docs/reference/clearExperiments.html
docs/reference/clearOptimizationParameters.html
docs/reference/clearParameterEstimationParameters.html
docs/reference/clearValidations.html
docs/reference/compileModel.html
docs/reference/convertToIrreversible.html
docs/reference/defineExperiments.html
docs/reference/defineOptimizationParameter.html
docs/reference/defineParameterEstimationParameter.html
docs/reference/deleteCompartment.html
docs/reference/deleteEvent.html
docs/reference/deleteGlobalQuantity.html
docs/reference/deleteKineticFunction.html
docs/reference/deleteReaction.html
docs/reference/deleteSpecies.html
docs/reference/entity_finders.html
docs/reference/figures/logo.png
docs/reference/figures/logo.svg
docs/reference/getAreaUnit.html
docs/reference/getCompartmentReferences.html
docs/reference/getCompartments.html
docs/reference/getCopasi.html
docs/reference/getCurrentModel.html
docs/reference/getEvents.html
docs/reference/getGlobalQuantities.html
docs/reference/getGlobalQuantityReferences.html
docs/reference/getInitialTime.html
docs/reference/getInitialValue.html
docs/reference/getLengthUnit.html
docs/reference/getLinearNoiseApproximationSettings.html
docs/reference/getLinkMatrix.html
docs/reference/getLoadedModels.html
docs/reference/getMetabolicControlAnalysisSettings.html
docs/reference/getModelName.html
docs/reference/getOptimizationSettings.html
docs/reference/getParameterEstimationSettings.html
docs/reference/getParameterReferences.html
docs/reference/getParameters.html
docs/reference/getQuantityUnit.html
docs/reference/getReactionMappings.html
docs/reference/getReactionReferences.html
docs/reference/getReactions.html
docs/reference/getReducedStoichiometryMatrix.html
docs/reference/getSpecies.html
docs/reference/getSpeciesReferences.html
docs/reference/getSteadyStateSettings.html
docs/reference/getStoichiometryMatrix.html
docs/reference/getTimeCourseSettings.html
docs/reference/getTimeUnit.html
docs/reference/getValidReactionFunctions.html
docs/reference/getValue.html
docs/reference/getVersion.html
docs/reference/getVolumeUnit.html
docs/reference/index.html
docs/reference/loadExamples.html
docs/reference/loadModel.html
docs/reference/loadModelFromString.html
docs/reference/loadSBML.html
docs/reference/loadSBMLFromString.html
docs/reference/newCompartment.html
docs/reference/newEvent.html
docs/reference/newGlobalQuantity.html
docs/reference/newKineticFunction.html
docs/reference/newModel.html
docs/reference/newReaction.html
docs/reference/newSpecies.html
docs/reference/openCopasi.html
docs/reference/regex.html
docs/reference/runLinearNoiseApproximation.html
docs/reference/runMetabolicControlAnalysis.html
docs/reference/runOptimization.html
docs/reference/runParameterEstimation.html
docs/reference/runSigmaPoint.html
docs/reference/runSteadyState.html
docs/reference/runTimeCourse.html
docs/reference/saveModel.html
docs/reference/saveModelToString.html
docs/reference/saveSBML.html
docs/reference/saveSBMLToString.html
docs/reference/setAreaUnit.html
docs/reference/setCompartments.html
docs/reference/setCurrentModel.html
docs/reference/setEvents.html
docs/reference/setGlobalQuantities.html
docs/reference/setInitialTime.html
docs/reference/setLengthUnit.html
docs/reference/setLinearNoiseApproximationSettings.html
docs/reference/setMetabolicControlAnalysisSettings.html
docs/reference/setModelName.html
docs/reference/setOptimizationSettings.html
docs/reference/setParameterEstimationSettings.html
docs/reference/setParameters.html
docs/reference/setQuantityUnit.html
docs/reference/setReactionFunction.html
docs/reference/setReactionMappings.html
docs/reference/setReactions.html
docs/reference/setSpecies.html
docs/reference/setSteadyStateSettings.html
docs/reference/setTimeCourseSettings.html
docs/reference/setTimeUnit.html
docs/reference/setVolumeUnit.html
docs/reference/unloadAllModels.html
docs/reference/unloadModel.html
docs/reference/updateInitialState.html
docs/sitemap.xml
inst/extdata/Kummer2000_Ca.xml
inst/extdata/brusselator.cps
inst/extdata/chemotaxis_4.cps
inst/extdata/test_names.cps
inst/extdata/test_paramest.cps
inst/extdata/test_paramest_exp_data.txt
man/CoRC-package.Rd man/addExperiments.Rd man/addOptimizationParameter.Rd man/addParameterEstimationParameter.Rd man/applyInitialState.Rd man/autoplot.copasi_ts.Rd man/clearCustomKineticFunctions.Rd man/clearExperiments.Rd man/clearOptimizationParameters.Rd man/clearParameterEstimationParameters.Rd man/clearValidations.Rd man/compileModel.Rd man/convertToIrreversible.Rd man/defineExperiments.Rd man/defineOptimizationParameter.Rd man/defineParameterEstimationParameter.Rd man/deleteCompartment.Rd man/deleteEvent.Rd man/deleteGlobalQuantity.Rd man/deleteKineticFunction.Rd man/deleteReaction.Rd man/deleteSpecies.Rd man/entity_finders.Rd
man/figures/logo.png
man/figures/logo.svg
man/getAreaUnit.Rd man/getCompartmentReferences.Rd man/getCompartments.Rd man/getCopasi.Rd man/getCurrentModel.Rd man/getEvents.Rd man/getGlobalQuantities.Rd man/getGlobalQuantityReferences.Rd man/getInitialTime.Rd man/getInitialValue.Rd man/getLengthUnit.Rd man/getLinearNoiseApproximationSettings.Rd man/getLinkMatrix.Rd man/getLoadedModels.Rd man/getMetabolicControlAnalysisSettings.Rd man/getModelName.Rd man/getOptimizationSettings.Rd man/getParameterEstimationSettings.Rd man/getParameterReferences.Rd man/getParameters.Rd man/getQuantityUnit.Rd man/getReactionMappings.Rd man/getReactionReferences.Rd man/getReactions.Rd man/getReducedStoichiometryMatrix.Rd man/getSpecies.Rd man/getSpeciesReferences.Rd man/getSteadyStateSettings.Rd man/getStoichiometryMatrix.Rd man/getTimeCourseSettings.Rd man/getTimeUnit.Rd man/getValidReactionFunctions.Rd man/getValue.Rd man/getVersion.Rd man/getVolumeUnit.Rd man/loadExamples.Rd man/loadModel.Rd man/loadModelFromString.Rd man/loadSBML.Rd man/loadSBMLFromString.Rd man/newCompartment.Rd man/newEvent.Rd man/newGlobalQuantity.Rd man/newKineticFunction.Rd man/newModel.Rd man/newReaction.Rd man/newSpecies.Rd man/openCopasi.Rd man/regex.Rd man/runLinearNoiseApproximation.Rd man/runMetabolicControlAnalysis.Rd man/runOptimization.Rd man/runParameterEstimation.Rd man/runSigmaPoint.Rd man/runSteadyState.Rd man/runTimeCourse.Rd man/saveModel.Rd man/saveModelToString.Rd man/saveSBML.Rd man/saveSBMLToString.Rd man/setAreaUnit.Rd man/setCompartments.Rd man/setCurrentModel.Rd man/setEvents.Rd man/setGlobalQuantities.Rd man/setInitialTime.Rd man/setLengthUnit.Rd man/setLinearNoiseApproximationSettings.Rd man/setMetabolicControlAnalysisSettings.Rd man/setModelName.Rd man/setOptimizationSettings.Rd man/setParameterEstimationSettings.Rd man/setParameters.Rd man/setQuantityUnit.Rd man/setReactionFunction.Rd man/setReactionMappings.Rd man/setReactions.Rd man/setSpecies.Rd man/setSteadyStateSettings.Rd man/setTimeCourseSettings.Rd man/setTimeUnit.Rd man/setVolumeUnit.Rd man/unloadAllModels.Rd man/unloadModel.Rd man/updateInitialState.Rd
tests/other/data/MAPKdata.txt
tests/other/test_biomodels.R tests/other/test_sigma_points.R tests/testthat.R tests/testthat/test_entity_accessors.R tests/testthat/test_entity_finders.R tests/testthat/test_expressions.R tests/testthat/test_misc.R tests/testthat/test_model_building.R tests/testthat/test_model_management.R tests/testthat/test_model_properties.R tests/testthat/test_task_lna.R tests/testthat/test_task_mca.R tests/testthat/test_task_optimization.R tests/testthat/test_task_parameterestimation.R tests/testthat/test_task_steadystate.R tests/testthat/test_task_timecourse.R tests/testthat/test_utils.R vignettes/CoRC.Rmd
vignettes/data/MAPKdata.txt
vignettes/entity_management.Rmd vignettes/examples.Rmd vignettes/issues.Rmd vignettes/model_building.Rmd vignettes/task_management.Rmd
jpahle/CoRC documentation built on Aug. 11, 2018, 1:10 p.m.