Files in ahgroup/DSAIRM
Dynamical Systems Approach to Immune Response Modeling

.Rbuildignore

.github/.gitignore

.github/workflows/R-CMD-check.yaml

.github/workflows/test-coverage.yaml

.gitignore

.nojekyll

DESCRIPTION

DSAIRM.Rproj

Meta/vignette.rds

NAMESPACE

NEWS.md R/DSAIRM-package.R R/check_simresults.R R/data.R R/dsairmmenu.R R/generate_documentation.R R/generate_fctcall.R R/generate_ggplot.R R/generate_modelsettings.R R/generate_plotly.R R/generate_shinyinput.R R/generate_text.R R/run_model.R R/simulate_acutevirusir_ode.R R/simulate_bacteria_fit.R R/simulate_basicbacteria_discrete.R R/simulate_basicbacteria_modelexploration.R R/simulate_basicbacteria_ode.R R/simulate_basicvirus_fit.R R/simulate_basicvirus_modelexploration.R R/simulate_basicvirus_ode.R R/simulate_basicvirus_stochastic.R R/simulate_chronicvirusir_ode.R R/simulate_confint_fit.R R/simulate_drugresistance_stochastic.R R/simulate_extendedbacteria_ode.R R/simulate_fludrug_fit.R R/simulate_modelcomparison_fit.R R/simulate_modelvariants_ode.R R/simulate_pkpdmodel_ode.R R/simulate_usanalysis.R R/simulate_virusandir_ode.R R/simulate_virusandtx_ode.R README.Rmd README.md

_pkgdown.yml

auxiliary/analytical_SS_computations/steadystate-bacteriamodel.wxm

auxiliary/analytical_SS_computations/steadystate-virusmodel.wxm

auxiliary/docsfordevelopers/documentation.md auxiliary/docsfordevelopers/notes-and-to-do.md auxiliary/docsfordevelopers/package-stats.R

auxiliary/dsairm_logo.svg

auxiliary/extdata/hayden96data.csv

auxiliary/helperfunctions/get_settings.R auxiliary/helperfunctions/processing_script.R auxiliary/helperfunctions/test-DSAIRMsolutions.R auxiliary/helperfunctions/write_tasktext.R auxiliary/oldfiles/DSAIRM.R auxiliary/oldfiles/app-with-dowload-code.R auxiliary/oldfiles/download_code.R

auxiliary/oldfiles/dsairm_references_old.bib

codecov.yml

cran-comments.md

data/hayden96flu.rda

data/schirm20strep.rda

doc/DSAIRM.R doc/DSAIRM.Rmd

doc/DSAIRM.html

docs/404.html

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docs/articles/DSAIRM.html

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docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/DSAIRM-package.html

docs/reference/Rplot001.png

docs/reference/check_simresults.html

docs/reference/dsairmmenu.html

docs/reference/figures/logo.png

docs/reference/generate_documentation.html

docs/reference/generate_fctcall.html

docs/reference/generate_ggplot.html

docs/reference/generate_modelsettings.html

docs/reference/generate_plotly.html

docs/reference/generate_shinyinput.html

docs/reference/generate_text.html

docs/reference/hayden96flu.html

docs/reference/index.html

docs/reference/run_model.html

docs/reference/schirm20strep.html

docs/reference/simulate_acutevirusir_ode-1.png

docs/reference/simulate_acutevirusir_ode.html

docs/reference/simulate_bacteria_fit.html

docs/reference/simulate_basicbacteria_discrete.html

docs/reference/simulate_basicbacteria_modelexploration-1.png

docs/reference/simulate_basicbacteria_modelexploration.html

docs/reference/simulate_basicbacteria_ode.html

docs/reference/simulate_basicvirus_fit.html

docs/reference/simulate_basicvirus_modelexploration-1.png

docs/reference/simulate_basicvirus_modelexploration.html

docs/reference/simulate_basicvirus_ode-1.png

docs/reference/simulate_basicvirus_ode.html

docs/reference/simulate_basicvirus_stochastic-1.png

docs/reference/simulate_basicvirus_stochastic.html

docs/reference/simulate_chronicvirusir_ode-1.png

docs/reference/simulate_chronicvirusir_ode.html

docs/reference/simulate_confint_fit.html

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docs/reference/simulate_drugresistance_stochastic.html

docs/reference/simulate_extendedbacteria_ode.html

docs/reference/simulate_fludrug_fit.html

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docs/reference/simulate_usanalysis-1.png

docs/reference/simulate_usanalysis.html

docs/reference/simulate_virusandir_ode-1.png

docs/reference/simulate_virusandir_ode.html

docs/reference/simulate_virusandtx_ode-1.png

docs/reference/simulate_virusandtx_ode.html

docs/sitemap.xml

inst/CITATION

inst/DSAIRM/app.R

inst/DSAIRM/google-analytics.html

inst/DSAIRM/packagestyle.css

inst/DSAIRM/rsconnect/shinyapps.io/epibiouga/dsairm.dcf

inst/appinformation/acutevirusir_documentation.Rmd

inst/appinformation/acutevirusir_documentation.html

inst/appinformation/acutevirusir_tasktable.tsv

inst/appinformation/apptable.tsv

inst/appinformation/basicbacteria_documentation.Rmd

inst/appinformation/basicbacteria_documentation.html

inst/appinformation/basicbacteria_tasktable.tsv

inst/appinformation/basicbacteriaexploration_documentation.Rmd

inst/appinformation/basicbacteriaexploration_documentation.html

inst/appinformation/basicbacteriaexploration_tasktable.tsv

inst/appinformation/basicvirus_documentation.Rmd

inst/appinformation/basicvirus_documentation.html

inst/appinformation/basicvirus_tasktable.tsv

inst/appinformation/basicvirusexploration_documentation.Rmd

inst/appinformation/basicvirusexploration_documentation.html

inst/appinformation/basicvirusexploration_tasktable.tsv

inst/appinformation/basicvirusstochastic_documentation.Rmd

inst/appinformation/basicvirusstochastic_documentation.html

inst/appinformation/basicvirusstochastic_tasktable.tsv

inst/appinformation/chronicvirusir_documentation.Rmd

inst/appinformation/chronicvirusir_documentation.html

inst/appinformation/chronicvirusir_tasktable.tsv

inst/appinformation/drugresistance_documentation.Rmd

inst/appinformation/drugresistance_documentation.html

inst/appinformation/drugresistance_tasktable.tsv

inst/appinformation/dsairm_references.bib

inst/appinformation/extendedbacteria_documentation.Rmd

inst/appinformation/extendedbacteria_documentation.html

inst/appinformation/extendedbacteria_tasktable.tsv

inst/appinformation/fitbacteria_documentation.Rmd

inst/appinformation/fitbacteria_documentation.html

inst/appinformation/fitbacteria_tasktable.tsv

inst/appinformation/fitbasicmodel_documentation.Rmd

inst/appinformation/fitbasicmodel_documentation.html

inst/appinformation/fitbasicmodel_tasktable.tsv

inst/appinformation/fitconfint_documentation.Rmd

inst/appinformation/fitconfint_documentation.html

inst/appinformation/fitconfint_tasktable.tsv

inst/appinformation/fitfludrug_documentation.Rmd

inst/appinformation/fitfludrug_documentation.html

inst/appinformation/fitfludrug_tasktable.tsv

inst/appinformation/fitmodelcomparison_documentation.Rmd

inst/appinformation/fitmodelcomparison_documentation.html

inst/appinformation/fitmodelcomparison_tasktable.tsv

inst/appinformation/modelvariants_documentation.Rmd

inst/appinformation/modelvariants_documentation.html

inst/appinformation/modelvariants_tasktable.tsv

inst/appinformation/pkpdmodel_documentation.Rmd

inst/appinformation/pkpdmodel_documentation.html

inst/appinformation/pkpdmodel_tasktable.tsv

inst/appinformation/startup_script.R inst/appinformation/usanalysis_documentation.Rmd

inst/appinformation/usanalysis_documentation.html

inst/appinformation/usanalysis_tasktable.tsv

inst/appinformation/virusandir_documentation.Rmd

inst/appinformation/virusandir_documentation.html

inst/appinformation/virusandir_tasktable.tsv

inst/appinformation/virusandtx_documentation.Rmd

inst/appinformation/virusandtx_documentation.html

inst/appinformation/virusandtx_tasktable.tsv

inst/mbmodels/Basic_Bacteria_model.Rds

inst/mbmodels/Basic_Virus_model.Rds

inst/media/acutevirusir.png

inst/media/acutevirusir.svg

inst/media/bacteriamodel.png

inst/media/bacteriamodel.svg

inst/media/chronicvirusir.png

inst/media/chronicvirusir.svg

inst/media/drugresistancemodel.png

inst/media/drugresistancemodel.svg

inst/media/dsairm_logo.png

inst/media/dsairm_logo.svg

inst/media/extendedbacteriamodel.png

inst/media/extendedbacteriamodel.svg

inst/media/fig1.png

inst/media/fig2.png

inst/media/fig3.png

inst/media/hcvdata.png

inst/media/hcvifndiagram.png

inst/media/hcvifndiagram.svg

inst/media/modelcomparison.png

inst/media/modelcomparison.svg

inst/media/modelvariants.png

inst/media/modelvariants.svg

inst/media/pkpdmodel.png

inst/media/pkpdmodel.svg

inst/media/virusandIRmodel.png

inst/media/virusandIRmodel.svg

inst/media/virusmodel.png

inst/media/virusmodel.svg

inst/simulatorfunctions/simulatorfunctions.zip

man/DSAIRM-package.Rd man/check_simresults.Rd man/dsairmmenu.Rd

man/figures/logo.png

man/generate_documentation.Rd man/generate_fctcall.Rd man/generate_ggplot.Rd man/generate_modelsettings.Rd man/generate_plotly.Rd man/generate_shinyinput.Rd man/generate_text.Rd man/hayden96flu.Rd man/run_model.Rd man/schirm20strep.Rd man/simulate_acutevirusir_ode.Rd man/simulate_bacteria_fit.Rd man/simulate_basicbacteria_discrete.Rd man/simulate_basicbacteria_modelexploration.Rd man/simulate_basicbacteria_ode.Rd man/simulate_basicvirus_fit.Rd man/simulate_basicvirus_modelexploration.Rd man/simulate_basicvirus_ode.Rd man/simulate_basicvirus_stochastic.Rd man/simulate_chronicvirusir_ode.Rd man/simulate_confint_fit.Rd man/simulate_drugresistance_stochastic.Rd man/simulate_extendedbacteria_ode.Rd man/simulate_fludrug_fit.Rd man/simulate_modelcomparison_fit.Rd man/simulate_modelvariants_ode.Rd man/simulate_pkpdmodel_ode.Rd man/simulate_usanalysis.Rd man/simulate_virusandir_ode.Rd man/simulate_virusandtx_ode.Rd

pkgdown/extra.css

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vignettes/mysimulator.R

vignettes/vignetterefs.bib

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ahgroup/DSAIRM documentation built on Oct. 4, 2023, 6:50 a.m.

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ahgroup/DSAIRM
Dynamical Systems Approach to Immune Response Modeling

Files in ahgroup/DSAIRM
Dynamical Systems Approach to Immune Response Modeling

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ahgroup/DSAIRM Dynamical Systems Approach to Immune Response Modeling

Files in ahgroup/DSAIRM Dynamical Systems Approach to Immune Response Modeling

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ahgroup/DSAIRM
Dynamical Systems Approach to Immune Response Modeling

Files in ahgroup/DSAIRM
Dynamical Systems Approach to Immune Response Modeling