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

.Rbuildignore
.gitignore
.travis.yml
CRAN-RELEASE
DESCRIPTION
DSAIRM.Rproj
NAMESPACE
NEWS.md R/DSAIRM.R R/dsairmmenu.R R/generate_documentation.R R/generate_fctcall.R R/generate_ggplot.R R/generate_plotly.R R/generate_shinyinput.R R/generate_text.R R/run_model.R R/simulate_basicbacteria_discrete.R R/simulate_basicbacteria_ode.R R/simulate_basicvirus_ode.R R/simulate_basicvirus_stochastic.R R/simulate_drugresistance_stochastic.R R/simulate_fit_basicmodel.R R/simulate_fit_confint.R R/simulate_fit_modelcomparison.R R/simulate_modelexploration.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.md
_pkgdown.yml
appveyor.yml
auxiliary/sismid-code/SISMID-U2-bacteria.r auxiliary/sismid-code/SISMID-U2-virus.r auxiliary/sismid-code/SISMID-U4-hcv1.r auxiliary/sismid-code/SISMID-U4-hcv2.r auxiliary/sismid-code/SISMID-U4-hcv3.r auxiliary/sismid-code/SISMID-U4-hcv4.r auxiliary/sismid-code/SISMID-U4-hiv1.r auxiliary/sismid-code/SISMID-U4-hiv2.r auxiliary/sismid-code/SISMID-U6-model1.r auxiliary/sismid-code/SISMID-U6-us1.r auxiliary/sismid-code/SISMID-U6-us2.r auxiliary/sismid-code/SISMID-U6-us3.r auxiliary/sismid-code/SISMID-U8-aic.r auxiliary/sismid-code/SISMID-U8-basic.r auxiliary/sismid-code/SISMID-U8-boot.r auxiliary/sismid-code/SISMID-U8-testing.r auxiliary/sismid-code/SISMID-U9-evolution.r auxiliary/sismid-code/SISMID-U9-memory.r auxiliary/sismid-code/SISMID-U9-noise.r auxiliary/sismid-code/vaccine-model.r
codecov.yml
cran-comments.md
docs/articles/DSAIRM.html
docs/articles/DSAIRM_files/figure-html/unnamed-chunk-13-1.png
docs/articles/DSAIRM_files/figure-html/unnamed-chunk-14-1.png
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docs/articles/DSAIRM_files/figure-html/unnamed-chunk-9-1.png
docs/articles/appexample.png
docs/articles/dsairmvignettestyle.css
docs/articles/index.html
docs/articles/mainmenu.png
docs/articles/modelexample.png
docs/articles/whattodoexample.png
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/extra.css
docs/index.html
docs/link.svg
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/DSAIRM.html
docs/reference/dsairmapps.html
docs/reference/dsairmmenu.html
docs/reference/generate_documentation.html
docs/reference/generate_fctcall.html
docs/reference/generate_ggplot.html
docs/reference/generate_instruction_tabs.html
docs/reference/generate_plotly.html
docs/reference/generate_plots.html
docs/reference/generate_shinyinput.html
docs/reference/generate_text.html
docs/reference/index.html
docs/reference/run_model.html
docs/reference/simulate_basicbacteria-1.png
docs/reference/simulate_basicbacteria.html
docs/reference/simulate_basicbacteria_discrete-1.png
docs/reference/simulate_basicbacteria_discrete.html
docs/reference/simulate_basicbacteria_ode.html
docs/reference/simulate_basicmodel_fit.html
docs/reference/simulate_basicvirus-1.png
docs/reference/simulate_basicvirus.html
docs/reference/simulate_basicvirus_ode.html
docs/reference/simulate_basicvirus_stochastic-1.png
docs/reference/simulate_basicvirus_stochastic.html
docs/reference/simulate_confint_fit.html
docs/reference/simulate_drugresistance-1.png
docs/reference/simulate_drugresistance.html
docs/reference/simulate_drugresistance_stochastic-1.png
docs/reference/simulate_drugresistance_stochastic.html
docs/reference/simulate_fit_basicmodel.html
docs/reference/simulate_fit_confint.html
docs/reference/simulate_fit_modelcomparison.html
docs/reference/simulate_fitbasicmodel.html
docs/reference/simulate_fitconfint.html
docs/reference/simulate_fitmodelcomparison.html
docs/reference/simulate_modelcomparison_fit.html
docs/reference/simulate_modelexploration-1.png
docs/reference/simulate_modelexploration.html
docs/reference/simulate_modelvariants-1.png
docs/reference/simulate_modelvariants.html
docs/reference/simulate_modelvariants_ode-1.png
docs/reference/simulate_modelvariants_ode.html
docs/reference/simulate_pkpdmodel-1.png
docs/reference/simulate_pkpdmodel.html
docs/reference/simulate_pkpdmodel_ode-1.png
docs/reference/simulate_pkpdmodel_ode.html
docs/reference/simulate_stochasticvirus-1.png
docs/reference/simulate_stochasticvirus.html
docs/reference/simulate_usanalysis-1.png
docs/reference/simulate_usanalysis.html
docs/reference/simulate_virus_tx-1.png
docs/reference/simulate_virus_tx.html
docs/reference/simulate_virusandir-1.png
docs/reference/simulate_virusandir.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/DSAIRM/app.R
inst/DSAIRM/packagestyle.css
inst/DSAIRM/rsconnect/shinyapps.io/epibiouga/dsairm.dcf
inst/appinformation/basicbacteria_documentation.Rmd
inst/appinformation/basicbacteria_documentation.html
inst/appinformation/basicbacteria_settings.R inst/appinformation/basicmodelfit_documentation.Rmd
inst/appinformation/basicmodelfit_documentation.html
inst/appinformation/basicmodelfit_settings.R inst/appinformation/basicvirus_documentation.Rmd
inst/appinformation/basicvirus_documentation.html
inst/appinformation/basicvirus_settings.R inst/appinformation/basicvirusstochastic_documentation.Rmd
inst/appinformation/basicvirusstochastic_documentation.html
inst/appinformation/basicvirusstochastic_settings.R inst/appinformation/confintfit_documentation.Rmd
inst/appinformation/confintfit_documentation.html
inst/appinformation/confintfit_settings.R inst/appinformation/drugresistance_documentation.Rmd
inst/appinformation/drugresistance_documentation.html
inst/appinformation/drugresistance_settings.R inst/appinformation/modelcomparisonfit_documentation.Rmd
inst/appinformation/modelcomparisonfit_documentation.html
inst/appinformation/modelcomparisonfit_settings.R inst/appinformation/modelexploration_documentation.Rmd
inst/appinformation/modelexploration_documentation.html
inst/appinformation/modelexploration_settings.R inst/appinformation/modelvariants_documentation.Rmd
inst/appinformation/modelvariants_documentation.html
inst/appinformation/modelvariants_settings.R inst/appinformation/pkpdmodel_documentation.Rmd
inst/appinformation/pkpdmodel_documentation.html
inst/appinformation/pkpdmodel_settings.R
inst/appinformation/references.bib
inst/appinformation/usanalysis_documentation.Rmd
inst/appinformation/usanalysis_documentation.html
inst/appinformation/usanalysis_settings.R inst/appinformation/virusandir_documentation.Rmd
inst/appinformation/virusandir_documentation.html
inst/appinformation/virusandir_settings.R inst/appinformation/virusandtx_documentation.Rmd
inst/appinformation/virusandtx_documentation.html
inst/appinformation/virusandtx_settings.R
inst/docsfordevelopers/documentation.html
inst/docsfordevelopers/documentation.md
inst/docsfordevelopers/rsconnect/shinyapps.io/handelgroup/docsfordevelopers.dcf
inst/extdata/hayden96data.csv
inst/media/bacteriamodel.png
inst/media/bacteriamodel.svg
inst/media/drugresistancemodel.png
inst/media/drugresistancemodel.svg
inst/media/fig1.png
inst/media/fig2.png
inst/media/fig3.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/virusdiagram.png
inst/media/virusdiagram.svg
inst/simulatorfunctions/simulate_basicbacteria_discrete.R inst/simulatorfunctions/simulate_basicbacteria_ode.R inst/simulatorfunctions/simulate_basicvirus_ode.R inst/simulatorfunctions/simulate_basicvirus_stochastic.R inst/simulatorfunctions/simulate_drugresistance_stochastic.R inst/simulatorfunctions/simulate_fit_basicmodel.R inst/simulatorfunctions/simulate_fit_confint.R inst/simulatorfunctions/simulate_fit_modelcomparison.R inst/simulatorfunctions/simulate_modelexploration.R inst/simulatorfunctions/simulate_modelvariants_ode.R inst/simulatorfunctions/simulate_pkpdmodel_ode.R inst/simulatorfunctions/simulate_usanalysis.R inst/simulatorfunctions/simulate_virusandir_ode.R inst/simulatorfunctions/simulate_virusandtx_ode.R
inst/simulatorfunctions/simulatorfunctions.zip
man/DSAIRM.Rd man/dsairmmenu.Rd man/generate_documentation.Rd man/generate_fctcall.Rd man/generate_ggplot.Rd man/generate_plotly.Rd man/generate_shinyinput.Rd man/generate_text.Rd man/run_model.Rd man/simulate_basicbacteria_discrete.Rd man/simulate_basicbacteria_ode.Rd man/simulate_basicvirus_ode.Rd man/simulate_basicvirus_stochastic.Rd man/simulate_drugresistance_stochastic.Rd man/simulate_fit_basicmodel.Rd man/simulate_fit_confint.Rd man/simulate_fit_modelcomparison.Rd man/simulate_modelexploration.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
tests/testthat.R tests/testthat/test-fit-apps.R tests/testthat/test-generate_documentation.R tests/testthat/test-generate_ggplot.R tests/testthat/test-generate_plotly.R tests/testthat/test-generate_shinyinput.R tests/testthat/test-generate_text.R tests/testthat/test-generate_usplot.R tests/testthat/test-modelexploration.R tests/testthat/test-run_model.R tests/testthat/test-stochastic-virus-app.R vignettes/DSAIRM.Rmd
vignettes/appexample.png
vignettes/mainmenu.png
vignettes/modelexample.png
vignettes/mysimulator.R
vignettes/vignetterefs.bib
vignettes/whattodoexample.png
ahgroup/DSAIRM documentation built on July 9, 2019, 8:02 a.m.