Files in Open-Systems-Pharmacology/OSPSuite.ReportingEngine
R package to create reports for the Open Systems Pharmacology models

.Rbuildignore

.gitattributes

.github/.gitignore

.github/workflows/Check_utf8.yml

.github/workflows/Dockerfile

.github/workflows/LinuxImages.yml

.github/workflows/codecov-nightly.yml

.github/workflows/install_dependencies.R

.github/workflows/install_packages_bionic.sh

.github/workflows/install_packages_centos7.sh

.github/workflows/install_packages_cran.sh

.github/workflows/install_prereq_bionic.sh

.github/workflows/install_prereq_centos7.sh

.github/workflows/lint.yaml

.github/workflows/pkgdown_setup.R .github/workflows/run_lintr.R .github/workflows/testRE.R

.github/workflows/update-dev-website.yml

.github/workflows/update-release-website.yml

.gitignore

.gitmodules

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/calculate-pk-parameters-task.R R/captions.R R/configuration-plan.R R/data-source.R R/error-checks.R R/excel-messages.R R/filenames-nomenclature.R R/globals.R R/gof-plot-task.R R/logging.R R/mean-model-workflow.R R/messages.R R/output.R R/pk-parameter-info.R R/plot-task.R R/population-plot-task.R R/population-sensitivity-analysis-task.R R/population-simulation-set.R R/population-study-design.R R/population-workflow.R R/qualification-comparison-time-profile.R R/qualification-ddi.R R/qualification-gof.R R/qualification-outputs.R R/qualification-pk-ratio.R R/qualification-task.R R/qualification-time-profile.R R/qualification-version-info.R R/qualification-workflow.R R/reportingengine-env.R R/sensitivity-analysis-settings.R R/sensitivity-analysis-task.R R/sensitivity-plot-settings.R R/simulation-set.R R/simulation-settings.R R/simulation-structure.R R/simulation-task.R R/system-info.R R/task-results.R R/task-settings.R R/task.R R/utilities-absorption.R R/utilities-calculate-pk-parameters.R R/utilities-configuration-plan.R R/utilities-demography.R R/utilities-excel-input.R R/utilities-goodness-of-fit.R R/utilities-logging.R R/utilities-mass-balance.R R/utilities-mpi-error-handling.R R/utilities-observed-data.R R/utilities-plots.R R/utilities-pop-pk-parameters.R R/utilities-qualification.R R/utilities-ratio-comparison.R R/utilities-reportingengine-env.R R/utilities-sensitivity-analysis.R R/utilities-simulation-set.R R/utilities-simulation.R R/utilities-task.R R/utilities-tracelib.R R/utilities-user-helpers.R R/utilities-workflow.R R/utilities-writing-report.R R/utils.R R/workflow.R README.md

_pkgdown.yml

appveyor.yml

inst/WORDLIST

inst/extdata/Aciclovir.pkml

inst/extdata/LarPop10.csv

inst/extdata/MiniModel1.pkml

inst/extdata/MiniModel2.pkml

inst/extdata/Pop200_p1p2p3.csv

inst/extdata/Pop500_p1p2p3.csv

inst/extdata/RalPop10.csv

inst/extdata/RaltegravirSim.pkml

inst/extdata/SimpleData.nmdat

inst/extdata/StudyDesign.csv

inst/extdata/WorkflowInput.xlsx

inst/extdata/adults.csv

inst/extdata/caffeine-simulation.pkml

inst/extdata/children.csv

inst/extdata/default-docx-configuration.txt

inst/extdata/mass-balance-settings.json

inst/extdata/mean-model-workflow-input-and-tasks.png

inst/extdata/obsPop.csv

inst/extdata/paragraph-styles-reference-doc.mp4

inst/extdata/pop1.csv

inst/extdata/pop2.csv

inst/extdata/popDictionary.csv

inst/extdata/population-workflow-input-and-tasks.png

inst/extdata/qualification-axis-settings.json

inst/extdata/qualification-workflow-template.R

inst/extdata/re-env.RData

inst/extdata/re-theme.json

inst/extdata/reference-docx.PNG

inst/extdata/reference.docx

inst/extdata/report-reference-docx.PNG

inst/extdata/sa-file-index.png

inst/extdata/sa-file-outputs.png

inst/extdata/table-style-reference-doc.mp4

inst/extdata/tpDictionary.csv

inst/extdata/tpDictionaryLoq.csv

ospsuite.reportingengine.Rproj

rakefile.rb

tests/data/absorption/Larson-Raltegravir.csv

tests/data/configuration-plan/duplicate-mappings.json

tests/data/configuration-plan/duplicate-obs-data.json

tests/data/configuration-plan/duplicate-sections.json

tests/data/configuration-plan/minimal.json

tests/data/configuration-plan/observed-datasets.csv

tests/data/configuration-plan/sections.csv

tests/data/configuration-plan/simulation-mappings.csv

tests/data/configuration-plan/wrong-field.json

tests/data/excel/template-bad-ids.xlsx

tests/data/excel/template-bad-output.xlsx

tests/data/excel/template-no-output.xlsx

tests/data/excel/template-no-source.xlsx

tests/data/excel/template-output.xlsx

tests/data/excel/template-source.xlsx

tests/data/input-data/LarPop10.csv

tests/data/input-data/Larson 2013 8-18y meal-Population.csv

tests/data/input-data/Larson 2013 8-18y meal.pkml

tests/data/input-data/MiniModel2.pkml

tests/data/input-data/Pop500_p1p2p3.csv

tests/data/input-data/RalPop10.csv

tests/data/input-data/Raltegravir Adult Population.csv

tests/data/input-data/RaltegravirSim.pkml

tests/data/input-data/SimpleData.nmdat

tests/data/input-data/SimpleDataWithLLOQ.nmdat

tests/data/input-data/SimpleDataWithUnit.nmdat

tests/data/input-data/StudyDesign.csv

tests/data/input-data/error-data.csv

tests/data/input-data/individualPksimSim.pkml

tests/data/input-data/popData.csv

tests/data/input-data/popData_short.csv

tests/data/input-data/simpleMobiEventSim.pkml

tests/data/input-data/tpDictionary-ill-defined-unit.csv

tests/data/input-data/tpDictionary-ill-defined-variable.csv

tests/data/input-data/tpDictionary-lloq.csv

tests/data/input-data/tpDictionary-unit-in-obs.csv

tests/data/input-data/tpDictionary.csv

tests/data/mass-balance/Larson-timeProfiles.csv

tests/data/mean-gof/All-Obs-residuals-lin.csv

tests/data/mean-gof/All-Obs-residuals.csv

tests/data/mean-gof/All-Obs-timeProfileData.csv

tests/data/mean-gof/No-Obs-timeProfileData.csv

tests/data/mean-gof/Select-Obs-residuals.csv

tests/data/mean-gof/Select-Obs-timeProfileData.csv

tests/data/mean-gof/lloq-timeProfileData.csv

tests/data/mean-pk/A-pkAnalysis-updatedPK.csv

tests/data/mean-pk/A-pkAnalysis.csv

tests/data/mean-sensitivity/A-SensitivityAnalysisResults.csv

tests/data/pop-gof/All-Obs-residuals.csv

tests/data/pop-gof/All-Obs-simulatedData.csv

tests/data/pop-gof/No-Obs-simulatedData.csv

tests/data/pop-gof/Select-Obs-residuals.csv

tests/data/pop-gof/Select-Obs-simulatedData.csv

tests/data/pop-pk/1_pk_parameters_AUC_tEnd.csv

tests/data/pop-pk/2_pk_parameters_AUC_tEnd.csv

tests/data/pop-pk/4_pk_parameters_C_max.csv

tests/data/pop-pk/5_pk_parameters_C_max.csv

tests/data/pop-sensitivity/A-SensitivityAnalysisResultsIndividualId-3.csv

tests/data/pop-sensitivity/A-SensitivityAnalysisResultsIndividualId-49.csv

tests/data/pop-sensitivity/A-SensitivityAnalysisResultsIndividualId-56.csv

tests/data/pop-sensitivity/A-popSensitivityResultsIndex.csv

tests/data/qualification/Content/images/images1/testcontent2.md tests/data/qualification/Content/images/testcontent1.md tests/data/qualification/Content/testcontent.md tests/data/qualification/Inputs/input.md tests/data/qualification/Intro/titlepage.md

tests/data/qualification/Models/Larson 2013 8-18y meal.pkml

tests/data/qualification/Models/MiniModel2.pkml

tests/data/qualification/ObservedData/DDI.csv

tests/data/qualification/ObservedData/MiniObs2.csv

tests/data/qualification/ObservedData/Parameters.csv

tests/data/qualification/ObservedData/test-data-semicolon-sep-dec-comma.csv

tests/data/qualification/configuration-plan-ddi-ratio.json

tests/data/qualification/configuration-plan-pk-ratio.json

tests/data/qualification/configuration-plan.json

tests/data/qualification/report-configuration-plan.json

tests/data/ratio-comparison/10_pk_parameters_C_max.csv

tests/data/ratio-comparison/11_pk_parameters_C_max.csv

tests/data/ratio-comparison/12_pk_ratios_C_max.csv

tests/data/ratio-comparison/1_pk_parameters_AUC_tEnd.csv

tests/data/ratio-comparison/2_pk_parameters_AUC_tEnd.csv

tests/data/ratio-comparison/3_pk_ratios_AUC_tEnd.csv

tests/data/ratio-comparison/4_pk_parameters_C_max.csv

tests/data/ratio-comparison/5_pk_parameters_C_max.csv

tests/data/ratio-comparison/6_pk_ratios_C_max.csv

tests/data/ratio-comparison/7_pk_parameters_AUC_tEnd.csv

tests/data/ratio-comparison/8_pk_parameters_AUC_tEnd.csv

tests/data/ratio-comparison/9_pk_ratios_AUC_tEnd.csv

tests/data/utilities-report/figureLinks.md tests/data/utilities-report/initialReport.md tests/data/utilities-report/testReportNumFigs.md tests/data/utilities-report/testReportNumSecs.md tests/data/utilities-report/testReportNumToc.md tests/data/utilities-report/titlepage.md tests/data/utilities-report/updatedtitlepage.md

tests/dev/01_MeanModel_Raltegravir/PKML/Raltegravir 10 mg (lactose formulation).pkml

tests/dev/01_MeanModel_Raltegravir/PKML/Raltegravir 50 mg (lactose formulation).pkml

tests/dev/01_MeanModel_Raltegravir/Raltegravir_PK.csv

tests/dev/01_MeanModel_Raltegravir/tpDictionary.csv

tests/dev/01_MeanModel_Raltegravir/workflow-input-01.xlsx

tests/dev/03_Population_Pediatric_Raltegavir/Larson 2013 8-18y meal-Population.csv

tests/dev/03_Population_Pediatric_Raltegavir/PKML/Larson 2013 8-18y meal.pkml

tests/dev/03_Population_Pediatric_Raltegavir/PKML/Raltegravir 400mg filmcoated tablet.pkml

tests/dev/03_Population_Pediatric_Raltegavir/Raltegravir Adult Population.csv

tests/dev/03_Population_Pediatric_Raltegavir/Raltegravir_PK.csv

tests/dev/03_Population_Pediatric_Raltegavir/StudyDesign.csv

tests/dev/03_Population_Pediatric_Raltegavir/test-example-03-demography.R tests/dev/03_Population_Pediatric_Raltegavir/test-example-03-goodness-of-fit.R tests/dev/03_Population_Pediatric_Raltegavir/test-example-03-pk-parameters.R tests/dev/03_Population_Pediatric_Raltegavir/test-example-03-user-defined.R tests/dev/03_Population_Pediatric_Raltegavir/test-example-03.R tests/dev/03_Population_Pediatric_Raltegavir/test-study-design.R

tests/dev/03_Population_Pediatric_Raltegavir/tpDictionary.csv

tests/dev/Qualification-Minimal/reporting engine input/Content/Section1.md tests/dev/Qualification-Minimal/reporting engine input/Content/Section2.1.md tests/dev/Qualification-Minimal/reporting engine input/Content/Section2.md tests/dev/Qualification-Minimal/reporting engine input/Inputs/Midazolam/Compound/Midazolam.md tests/dev/Qualification-Minimal/reporting engine input/Inputs/Midazolam/Simulation/S1.md tests/dev/Qualification-Minimal/reporting engine input/Intro/intro.md tests/dev/Qualification-Minimal/reporting engine input/Intro/remote_intro.md

tests/dev/Qualification-Minimal/reporting engine input/Itraconazole/S1/S1.pkml

tests/dev/Qualification-Minimal/reporting engine input/Itraconazole/S1/S1.xml

tests/dev/Qualification-Minimal/reporting engine input/Midazolam/S1/S1.pkml

tests/dev/Qualification-Minimal/reporting engine input/Midazolam/S1/S1.xml

tests/dev/Qualification-Minimal/reporting engine input/Midazolam/S2/S2.pkml

tests/dev/Qualification-Minimal/reporting engine input/Midazolam/S2/S2.xml

tests/dev/Qualification-Minimal/reporting engine input/ObservedData/DDI_Ratio_CYP3A4.csv

tests/dev/Qualification-Minimal/reporting engine input/ObservedData/Itraconazole 600mg MD.csv

tests/dev/Qualification-Minimal/reporting engine input/ObservedData/Itraconazole 600mg MD.xlsx

tests/dev/Qualification-Minimal/reporting engine input/ObservedData/Midazolam 600mg SD.csv

tests/dev/Qualification-Minimal/reporting engine input/ObservedData/Midazolam 600mg SD.xlsx

tests/dev/Qualification-Minimal/reporting engine input/report-configuration-plan.json

tests/dev/Qualification-Minimal/reporting engine output/SimulationResults/Itraconazole-S1-SimulationResults.csv

tests/dev/Qualification-Minimal/reporting engine output/SimulationResults/Midazolam-S1-SimulationResults.csv

tests/dev/Qualification-Minimal/reporting engine output/SimulationResults/Midazolam-S2-SimulationResults.csv

tests/dev/Qualification-Minimal/reporting engine output/TimeProfiles/Itraconazole-S1-timeProfile-Concentration-total.png

tests/dev/Qualification-Minimal/reporting engine output/TimeProfiles/Itraconazole-S1-timeProfile-Fraction-total.png

tests/dev/Qualification-Minimal/reporting engine output/TimeProfiles/Itraconazole-S1-timeProfileData.csv

tests/dev/Qualification-Minimal/reporting engine output/TimeProfiles/Itraconazole-S1-timeProfileLog-Concentration-total.png

tests/dev/Qualification-Minimal/reporting engine output/TimeProfiles/Itraconazole-S1-timeProfileLog-Fraction-total.png

tests/dev/Qualification-Minimal/reporting engine output/TimeProfiles/Midazolam-S2-timeProfile-Concentration-total.png

tests/dev/Qualification-Minimal/reporting engine output/TimeProfiles/Midazolam-S2-timeProfileData.csv

tests/dev/Qualification-Minimal/reporting engine output/TimeProfiles/Midazolam-S2-timeProfileLog-Concentration-total.png

tests/dev/Qualification-Minimal/reporting engine output/appendix-time-profile-usedFiles.txt

tests/dev/Qualification-Minimal/reporting engine output/appendix-time-profile.md

tests/dev/Qualification-Minimal/reporting engine output/log-debug.txt

tests/dev/Qualification-Minimal/reporting engine output/log-info.txt

tests/dev/Qualification-Minimal/test-ddi.R tests/dev/Qualification-Minimal/test-qualplot.R tests/dev/Qualification-Minimal/test-residuals.R tests/dev/Qualification-Minimal/test-workflow.R

tests/dev/myWorkflowPreviousResults/SimulationResults/Raltegravir 50 mg (lactose formulation)-SimulationResults.csv

vignettes/.gitignore

vignettes/add-title-page.Rmd vignettes/demography.Rmd vignettes/excel-template.Rmd

vignettes/figures/mean-model-workflow-input-and-tasks.png

vignettes/figures/paragraph-styles-reference-doc.mp4

vignettes/figures/population-workflow-input-and-tasks.png

vignettes/figures/reference-docx.png

vignettes/figures/report-reference-docx.png

vignettes/figures/report-snapshot-1.png

vignettes/figures/report-snapshot-10.png

vignettes/figures/report-snapshot-11.png

vignettes/figures/report-snapshot-12.png

vignettes/figures/report-snapshot-13.png

vignettes/figures/report-snapshot-14.png

vignettes/figures/report-snapshot-15.png

vignettes/figures/report-snapshot-16.png

vignettes/figures/report-snapshot-17.png

vignettes/figures/report-snapshot-18.png

vignettes/figures/report-snapshot-19.png

vignettes/figures/report-snapshot-2.png

vignettes/figures/report-snapshot-22.png

vignettes/figures/report-snapshot-23.png

vignettes/figures/report-snapshot-24.png

vignettes/figures/report-snapshot-25.png

vignettes/figures/report-snapshot-26.png

vignettes/figures/report-snapshot-27.png

vignettes/figures/report-snapshot-28.png

vignettes/figures/report-snapshot-29.png

vignettes/figures/report-snapshot-3.png

vignettes/figures/report-snapshot-30.png

vignettes/figures/report-snapshot-31.png

vignettes/figures/report-snapshot-32.png

vignettes/figures/report-snapshot-35.png

vignettes/figures/report-snapshot-4.png

vignettes/figures/report-snapshot-5.png

vignettes/figures/report-snapshot-6.png

vignettes/figures/report-snapshot-7.png

vignettes/figures/report-snapshot-8.png

vignettes/figures/report-snapshot-9.png

vignettes/figures/sa-file-index.png

vignettes/figures/sa-file-outputs.png

vignettes/figures/table-style-reference-doc.mp4

vignettes/goodness-of-fit.Rmd vignettes/mass-balance.Rmd

vignettes/my-new-theme.json

vignettes/ospsuite-reportingengine.Rmd vignettes/pk-parameters.Rmd vignettes/plot-settings.Rmd vignettes/pop-pk-parameters.Rmd vignettes/qualification-workflow.Rmd vignettes/sensitivity-analysis.Rmd vignettes/word-report.Rmd

Open-Systems-Pharmacology/OSPSuite.ReportingEngine documentation built on May 1, 2024, 12:27 p.m.

rdrr.io home R language documentation Run R code online

CRAN packages Bioconductor packages R-Forge packages GitHub packages

Note that we can't provide technical support on individual packages. You should contact the package authors for that.

Open-Systems-Pharmacology/OSPSuite.ReportingEngine
R package to create reports for the Open Systems Pharmacology models

Files in Open-Systems-Pharmacology/OSPSuite.ReportingEngine
R package to create reports for the Open Systems Pharmacology models

R Package Documentation

Browse R Packages

We want your feedback!

Open-Systems-Pharmacology/OSPSuite.ReportingEngine R package to create reports for the Open Systems Pharmacology models

Files in Open-Systems-Pharmacology/OSPSuite.ReportingEngine R package to create reports for the Open Systems Pharmacology models

R Package Documentation

Browse R Packages

We want your feedback!

Open-Systems-Pharmacology/OSPSuite.ReportingEngine
R package to create reports for the Open Systems Pharmacology models

Files in Open-Systems-Pharmacology/OSPSuite.ReportingEngine
R package to create reports for the Open Systems Pharmacology models