Files in jpahle/CoRC
COPASI R Connector
.Rbuildignore
.gitignore
.gitmodules
CoRC.Rproj
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/CoRC.R
R/deprecated.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
dev/auto_tester/README
dev/auto_tester/container_copasi_dev/Dockerfile
dev/auto_tester/container_copasi_release/Dockerfile
dev/auto_tester/container_r_devel/Dockerfile
dev/auto_tester/container_r_latest/Dockerfile
dev/auto_tester/container_r_var/Dockerfile
dev/auto_tester/container_r_var/biomodels_test.sh
dev/auto_tester/container_r_var/full_test.sh
dev/auto_tester/container_r_var/quick_test.sh
dev/auto_tester/container_r_var/test_lib_with_rX.sh
dev/auto_tester/test_copasi_dev_biomodels.sh
dev/auto_tester/test_copasi_dev_pkg.sh
dev/auto_tester/test_copasi_release_biomodels.sh
dev/auto_tester/test_copasi_release_pkg.sh
dev/auto_tester/test_lib_with_r_var.sh
dev/auto_tester/test_master_with_r_devel.sh
dev/auto_tester/test_master_with_r_latest.sh
dev/compile_copasi.Rmd
dev/copasi-source/CopasiVersion.h
dev/copasi-source/build_darwin_x64_clean.sh
dev/copasi-source/build_darwin_x64_quick.sh
dev/copasi-source/build_linux_x64_clean.sh
dev/copasi-source/build_linux_x64_quick.sh
dev/copasi-source/build_windows_x64_clean.bat
dev/copasi-source/build_windows_x64_quick.bat
dev/copasi-source/compilers/centos6_x64/Dockerfile
dev/copasi-source/compilers/centos7_x64/Dockerfile
dev/copasi-source/compilers/centos8_x64/Dockerfile
dev/copasi-source/compilers/manylinux2010_x64/Dockerfile
dev/copasi-source/compilers/manylinux2014_x64/Dockerfile
dev/copasi-source/compilers/ubuntu2004_x64/Dockerfile
dev/copasi-source/compilers/windows_x64/Dockerfile
dev/copasi-source/compilers/windows_x64/r_lib_extractor/README
dev/copasi-source/compilers/windows_x64/r_lib_extractor/README.txt
dev/copasi-source/compilers/windows_x64/r_lib_extractor/expdef64.exe
dev/copasi-source/d_build_centos6_x64_clean.sh
dev/copasi-source/d_build_centos7_x64_clean.sh
dev/copasi-source/d_build_centos8_x64_clean.sh
dev/copasi-source/d_build_manylinux2010_x64_clean.ps1
dev/copasi-source/d_build_manylinux2010_x64_clean.sh
dev/copasi-source/d_build_manylinux2010_x64_quick.ps1
dev/copasi-source/d_build_manylinux2010_x64_quick.sh
dev/copasi-source/d_build_manylinux2014_x64_clean.ps1
dev/copasi-source/d_build_manylinux2014_x64_clean.sh
dev/copasi-source/d_build_manylinux2014_x64_quick.ps1
dev/copasi-source/d_build_manylinux2014_x64_quick.sh
dev/copasi-source/d_build_ubuntu2004_x64_clean.sh
dev/copasi-source/d_build_windows_x64_clean.ps1
dev/copasi-source/d_build_windows_x64_clean.sh
dev/copasi-source/d_build_windows_x64_quick.ps1
dev/copasi-source/d_build_windows_x64_quick.sh
dev/dev_documentation.Rmd
dev/dev_setup.Rmd
dev/dev_tools.R
dev/patch-swig-wrapper.R
dev/site_upgrade.R
dev/update-swig-in-package.R
docs/404.html
docs/LICENSE-text.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/CoRC.html
docs/articles/CoRC_files/figure-html/unnamed-chunk-11-1.png
docs/articles/entity_management.html
docs/articles/examples.html
docs/articles/examples_files/crosstalk-1.2.0/css/crosstalk.min.css
docs/articles/examples_files/crosstalk-1.2.0/js/crosstalk.js
docs/articles/examples_files/crosstalk-1.2.0/js/crosstalk.js.map
docs/articles/examples_files/crosstalk-1.2.0/js/crosstalk.min.js
docs/articles/examples_files/crosstalk-1.2.0/js/crosstalk.min.js.map
docs/articles/examples_files/crosstalk-1.2.0/scss/crosstalk.scss
docs/articles/examples_files/htmlwidgets-1.6.1/htmlwidgets.js
docs/articles/examples_files/plotly-binding-4.10.1/plotly.js
docs/articles/examples_files/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css
docs/articles/examples_files/plotly-main-2.11.1/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/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/docsearch.json
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/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/biomodels_url.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-deprecated.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/loadCombineArchive.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/saveCombineArchive.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/CITATION
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/biomodels_url.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-deprecated.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/loadCombineArchive.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/saveCombineArchive.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
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
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
