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-4.7)DSAIRM_0.9.7.zip(r-4.6)DSAIRM_0.9.7.zip(r-4.5)
DSAIRM_0.9.7.tgz(r-4.6-any)DSAIRM_0.9.7.tgz(r-4.5-any)
DSAIRM_0.9.7.tar.gz(r-4.7-any)DSAIRM_0.9.7.tar.gz(r-4.6-any)
DSAIRM_0.9.7.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DSAIRM/json (API)

# Install 'DSAIRM' in R:

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

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

Pkgdown/docs site:https://ahgroup.github.io

Datasets:

hayden96flu - Influenza virus load data
schirm20strep - Streptococcus pneumoniae infection data

On CRAN:

6.29 score 34 stars 29 scripts 310 downloads 1 mentions 30 exports 76 dependencies

Last updated from:62d9916da5. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	222
source / vignettes	OK	222
linux-release-x86_64	OK	200
macos-release-arm64	OK	170
macos-oldrel-arm64	OK	248
windows-devel	OK	191
windows-release	OK	163
windows-oldrel	OK	166
wasm-release	OK	142

Exports:check_simresults dsairmmenu generate_documentation generate_fctcall generate_ggplot generate_modelsettings generate_plotly generate_shinyinput generate_text run_model simulate_acutevirusir_ode simulate_bacteria_fit simulate_basicbacteria_discrete simulate_basicbacteria_modelexploration simulate_basicbacteria_ode simulate_basicvirus_fit simulate_basicvirus_modelexploration simulate_basicvirus_ode simulate_basicvirus_stochastic simulate_chronicvirusir_ode simulate_confint_fit simulate_drugresistance_stochastic simulate_extendedbacteria_ode simulate_fludrug_fit simulate_modelcomparison_fit simulate_modelvariants_ode simulate_pkpdmodel_ode simulate_usanalysis simulate_virusandir_ode simulate_virusandtx_ode

Dependencies:adaptivetau askpass base64enc boot bslib cachem cli commonmark cpp11 crosstalk curl data.table deSolve digest dplyr evaluate farver fastmap fontawesome fs generics ggplot2 glue gridExtra gtable highr htmltools htmlwidgets httpuv httr isoband jquerylib jsonlite knitr labeling later lazyeval lhs lifecycle magrittr memoise mime nloptr openssl otel pillar pkgconfig plotly promises purrr R6 rappdirs RColorBrewer Rcpp rlang rmarkdown S7 sass scales shiny sourcetools stringi stringr sys tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML xtable yaml

DSAIRM Package Tutorial

Rendered fromDSAIRM.Rmdusingknitr::rmarkdown

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

Help page	Topics
A function that checks if a call to simulation function worked	check_simresults
The main menu for the DSAIRM package	dsairmmenu
A helper function which processes and displays the documentation part for each app	generate_documentation
A helper function that produces a call to a simulator function for specific settings	generate_fctcall
A helper function that takes simulation results and produces ggplot plots	generate_ggplot
A function to parse modelsettings for simulation runs	generate_modelsettings
A helper function that takes simulation results and produces plotly plots	generate_plotly
A helper function that takes a model and generates shiny UI elements	generate_shinyinput
A helper function that takes result from the simulators and produces text output	generate_text
Influenza virus load data	hayden96flu
A function that runs an app for specific settings and processes results for plot and text generation	run_model
Streptococcus pneumoniae infection data	schirm20strep
Acute Virus Infection and IR Model	simulate_acutevirusir_ode
Fitting a simple bacteria infection models to Streptococcus pneumoniae infection data	simulate_bacteria_fit
Basic Bacteria model - discrete	simulate_basicbacteria_discrete
Simulation to illustrate parameter scan of the basic bacteria model #'	simulate_basicbacteria_modelexploration
Basic Bacteria model - ODE	simulate_basicbacteria_ode
Fitting a simple viral infection models to influenza data	simulate_basicvirus_fit
Simulation to illustrate parameter scan of the basic virus model #'	simulate_basicvirus_modelexploration
Basic Virus Model	simulate_basicvirus_ode
Basic Virus Model	simulate_basicvirus_stochastic
Chronic Virus Infection and IR Model	simulate_chronicvirusir_ode
Fit a simple viral infection model and compute confidence intervals	simulate_confint_fit
Stochastic simulation of a compartmental acute virus infection model with treatment and drug resistant strain	simulate_drugresistance_stochastic
Extended Bacteria model - ODE	simulate_extendedbacteria_ode
Fitting a simple viral infection model with 2 types of drug mechanisms to influenza data	simulate_fludrug_fit
Fitting 2 simple viral infection models to influenza data	simulate_modelcomparison_fit
Simulation of a viral infection model with immune response The simulation illustrates different alternative models.	simulate_modelvariants_ode
PkPd Virus model	simulate_pkpdmodel_ode
Simulation to illustrate uncertainty and sensitivity analysis	simulate_usanalysis
Simulation of a viral infection model with an immune response	simulate_virusandir_ode
Simulation of a basic viral infection model with drug treatment	simulate_virusandtx_ode

Package: DSAIRM 0.9.7

DSAIRM: Dynamical Systems Approach to Immune Response Modeling

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)