Package: DSAIDE 0.9.6

Andreas Handel

DSAIDE: Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution)

Exploration of simulation models (apps) of various infectious disease transmission dynamics scenarios. The purpose of the package is to help individuals learn about infectious disease epidemiology (ecology/evolution) 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], Isaac Chun-Hai Fung [ctb], Ronald Galiwango [ctb], Salil Goyal [ctb], Spencer Hall [ctb], Ben Listyg [ctb], Brian McKay [ctb], John Rossow [ctb], Sina Solaimanpour [ctb], Alexis Vittengl [ctb], Henok Woldu [ctb]

DSAIDE_0.9.6.tar.gz
DSAIDE_0.9.6.zip(r-4.7)DSAIDE_0.9.6.zip(r-4.6)DSAIDE_0.9.6.zip(r-4.5)
DSAIDE_0.9.6.tgz(r-4.6-any)DSAIDE_0.9.6.tgz(r-4.5-any)
DSAIDE_0.9.6.tar.gz(r-4.7-any)DSAIDE_0.9.6.tar.gz(r-4.6-any)
DSAIDE_0.9.6.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
DSAIDE/json (API)

# Install 'DSAIDE' in R:

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

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

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

Datasets:

flu1918data - 1918 Influenza mortality data
norodata - Cases of norovirus during an outbreak

On CRAN:

6.34 score 26 stars 24 scripts 400 downloads 1 mentions 30 exports 75 dependencies

Last updated from:85b5438144. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	188
source / vignettes	OK	282
linux-release-x86_64	OK	207
macos-release-arm64	OK	136
macos-oldrel-arm64	OK	137
windows-devel	OK	167
windows-release	OK	160
windows-oldrel	OK	154
wasm-release	OK	143

Exports:dsaidemenu generate_documentation generate_fctcall generate_ggplot generate_plotly generate_shinyinput generate_text run_model simulate_Characteristics_of_ID_ode simulate_Complex_ID_Control_ode simulate_directtransmission_ode simulate_Drug_Resistance_Evolution_stochastic simulate_Environmental_Transmission_model_ode simulate_flu_fit simulate_Host_Heterogeneity_Model_ode simulate_idcontrolmultigroup_ode simulate_idcontrolmultioutbreak_ode simulate_idpatterns_ode simulate_idsurveillance_ode simulate_idvaccine_ode simulate_multipathogen_ode simulate_noro_fit simulate_SEIRSd_model_stochastic simulate_SIR_model_discrete simulate_SIR_model_ode simulate_SIR_modelexploration simulate_SIR_usanalysis simulate_SIRSd_model_ode simulate_SIRSd_model_stochastic simulate_Vector_transmission_model_ode

Dependencies:adaptivetau askpass base64enc 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

DSAIDE Package Tutorial

Rendered fromDSAIDE.Rmdusingknitr::rmarkdown

Last update: 2023-08-22
Started: 2016-08-11

Help page	Topics
The main menu for the DSAIDE package	dsaidemenu
1918 Influenza mortality data	flu1918data
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 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
Cases of norovirus during an outbreak	norodata
A function that runs an app for specific settings and processes results for plot and text generation	run_model
Characteristics of ID	simulate_Characteristics_of_ID_ode
Complex ID Control	simulate_Complex_ID_Control_ode
Simulation of a compartmental infectious disease transmission model illustrating different types of direct transmission	simulate_directtransmission_ode
Drug Resistance Evolution	simulate_Drug_Resistance_Evolution_stochastic
Environmental Transmission model	simulate_Environmental_Transmission_model_ode
Fitting a SIR-type model to flu data	simulate_flu_fit
Host Heterogeneity Model	simulate_Host_Heterogeneity_Model_ode
Simulation of a compartmental infectious disease transmission model with 3 types of hosts and intervention	simulate_idcontrolmultigroup_ode
Simulation of a compartmental infectious disease transmission model to study the reproductive number	simulate_idcontrolmultioutbreak_ode
Simulation of a compartmental infectious disease transmission model including seasonality	simulate_idpatterns_ode
Simulation of a compartmental infectious disease transmission model illustrating the impact of ID surveillance	simulate_idsurveillance_ode
Simulation of a compartmental infectious disease transmission model to study the reproductive number	simulate_idvaccine_ode
Simulation of a compartmental infectious disease transmission model with 2 types of pathogens	simulate_multipathogen_ode
Fitting a simple SIR type model to norovirus outbreak data	simulate_noro_fit
SEIRSd model	simulate_SEIRSd_model_stochastic
SIR model	simulate_SIR_model_discrete
SIR model	simulate_SIR_model_ode
Simulation to illustrate parameter scan of the basic SIR model with births and deaths #'	simulate_SIR_modelexploration
Simulation to illustrate uncertainty and sensitivity analysis	simulate_SIR_usanalysis
SIRSd model	simulate_SIRSd_model_ode
SIRSd model	simulate_SIRSd_model_stochastic
Vector transmission model	simulate_Vector_transmission_model_ode

Package: DSAIDE 0.9.6

DSAIDE: Dynamical Systems Approach to Infectious Disease Epidemiology (Ecology/Evolution)

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Help Manual

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