Package: DSAIRM 0.9.7

Andreas Handel

DSAIRM: Dynamical Systems Approach to Immune Response Modeling

Simulation models (apps) of various within-host immune response scenarios. The purpose of the package is to help individuals learn about within-host infection and immune response modeling from a dynamical systems perspective. All apps include explanations of the underlying models and instructions on what to do with the models.

Authors:Andreas Handel [aut, cre], Cody Dailey [ctb], Yang Ge [ctb], Spencer Hall [ctb], Brian McKay [ctb], Sina Solaimanpour [ctb], Alexis Vittengl [ctb], Henok Woldu [ctb]

DSAIRM_0.9.7.tar.gz
DSAIRM_0.9.7.zip(r-4.5)DSAIRM_0.9.7.zip(r-4.4)DSAIRM_0.9.7.zip(r-4.3)
DSAIRM_0.9.7.tgz(r-4.4-any)DSAIRM_0.9.7.tgz(r-4.3-any)
DSAIRM_0.9.7.tar.gz(r-4.5-noble)DSAIRM_0.9.7.tar.gz(r-4.4-noble)
DSAIRM_0.9.7.tgz(r-4.4-emscripten)DSAIRM_0.9.7.tgz(r-4.3-emscripten)
DSAIRM.pdf |DSAIRM.html✨
DSAIRM/json (API)
NEWS

# Install 'DSAIRM' in R:
install.packages('DSAIRM', repos = c('https://ahgroup.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/ahgroup/dsairm/issues

Datasets:

On CRAN:

30 exports 32 stars 2.81 score 83 dependencies 1 mentions 23 scripts 315 downloads

Last updated 2 months agofrom:62d9916da5. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 17 2024
R-4.5-winOKSep 17 2024
R-4.5-linuxOKSep 17 2024
R-4.4-winOKSep 17 2024
R-4.4-macOKSep 17 2024
R-4.3-winOKSep 17 2024
R-4.3-macOKSep 17 2024

Exports:check_simresultsdsairmmenugenerate_documentationgenerate_fctcallgenerate_ggplotgenerate_modelsettingsgenerate_plotlygenerate_shinyinputgenerate_textrun_modelsimulate_acutevirusir_odesimulate_bacteria_fitsimulate_basicbacteria_discretesimulate_basicbacteria_modelexplorationsimulate_basicbacteria_odesimulate_basicvirus_fitsimulate_basicvirus_modelexplorationsimulate_basicvirus_odesimulate_basicvirus_stochasticsimulate_chronicvirusir_odesimulate_confint_fitsimulate_drugresistance_stochasticsimulate_extendedbacteria_odesimulate_fludrug_fitsimulate_modelcomparison_fitsimulate_modelvariants_odesimulate_pkpdmodel_odesimulate_usanalysissimulate_virusandir_odesimulate_virusandtx_ode

Dependencies:adaptivetauaskpassbase64encbootbslibcachemclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledeSolvedigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallhslifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmenloptropensslpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalesshinysourcetoolsstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLxtableyaml

DSAIRM Package Tutorial

Andreas Handel

Rendered fromDSAIRM.Rmdusingknitr::rmarkdownon Sep 17 2024.

Last update: 2023-10-02
Started: 2017-10-02

Readme and manuals

Help Manual

Help pageTopics
A function that checks if a call to simulation function workedcheck_simresults
The main menu for the DSAIRM packagedsairmmenu
A helper function which processes and displays the documentation part for each appgenerate_documentation
A helper function that produces a call to a simulator function for specific settingsgenerate_fctcall
A helper function that takes simulation results and produces ggplot plotsgenerate_ggplot
A function to parse modelsettings for simulation runsgenerate_modelsettings
A helper function that takes simulation results and produces plotly plotsgenerate_plotly
A helper function that takes a model and generates shiny UI elementsgenerate_shinyinput
A helper function that takes result from the simulators and produces text outputgenerate_text
Influenza virus load datahayden96flu
A function that runs an app for specific settings and processes results for plot and text generationrun_model
Streptococcus pneumoniae infection dataschirm20strep
Acute Virus Infection and IR Modelsimulate_acutevirusir_ode
Fitting a simple bacteria infection models to Streptococcus pneumoniae infection datasimulate_bacteria_fit
Basic Bacteria model - discretesimulate_basicbacteria_discrete
Simulation to illustrate parameter scan of the basic bacteria model #'simulate_basicbacteria_modelexploration
Basic Bacteria model - ODEsimulate_basicbacteria_ode
Fitting a simple viral infection models to influenza datasimulate_basicvirus_fit
Simulation to illustrate parameter scan of the basic virus model #'simulate_basicvirus_modelexploration
Basic Virus Modelsimulate_basicvirus_ode
Basic Virus Modelsimulate_basicvirus_stochastic
Chronic Virus Infection and IR Modelsimulate_chronicvirusir_ode
Fit a simple viral infection model and compute confidence intervalssimulate_confint_fit
Stochastic simulation of a compartmental acute virus infection model with treatment and drug resistant strainsimulate_drugresistance_stochastic
Extended Bacteria model - ODEsimulate_extendedbacteria_ode
Fitting a simple viral infection model with 2 types of drug mechanisms to influenza datasimulate_fludrug_fit
Fitting 2 simple viral infection models to influenza datasimulate_modelcomparison_fit
Simulation of a viral infection model with immune response The simulation illustrates different alternative models.simulate_modelvariants_ode
PkPd Virus modelsimulate_pkpdmodel_ode
Simulation to illustrate uncertainty and sensitivity analysissimulate_usanalysis
Simulation of a viral infection model with an immune responsesimulate_virusandir_ode
Simulation of a basic viral infection model with drug treatmentsimulate_virusandtx_ode