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-4.5)DSAIDE_0.9.6.zip(r-4.4)DSAIDE_0.9.6.zip(r-4.3)
DSAIDE_0.9.6.tgz(r-4.4-any)DSAIDE_0.9.6.tgz(r-4.3-any)
DSAIDE_0.9.6.tar.gz(r-4.5-noble)DSAIDE_0.9.6.tar.gz(r-4.4-noble)
DSAIDE_0.9.6.tgz(r-4.4-emscripten)DSAIDE_0.9.6.tgz(r-4.3-emscripten)
DSAIDE.pdf |DSAIDE.html✨
DSAIDE/json (API)
NEWS

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

Peer review:

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

Datasets:

On CRAN:

30 exports 24 stars 2.68 score 82 dependencies 1 mentions 22 scripts 458 downloads

Last updated 8 months agofrom:85b5438144. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKSep 12 2024
R-4.5-winOKSep 12 2024
R-4.5-linuxOKSep 12 2024
R-4.4-winOKSep 12 2024
R-4.4-macOKSep 12 2024
R-4.3-winOKSep 12 2024
R-4.3-macOKSep 12 2024

Exports:dsaidemenugenerate_documentationgenerate_fctcallgenerate_ggplotgenerate_plotlygenerate_shinyinputgenerate_textrun_modelsimulate_Characteristics_of_ID_odesimulate_Complex_ID_Control_odesimulate_directtransmission_odesimulate_Drug_Resistance_Evolution_stochasticsimulate_Environmental_Transmission_model_odesimulate_flu_fitsimulate_Host_Heterogeneity_Model_odesimulate_idcontrolmultigroup_odesimulate_idcontrolmultioutbreak_odesimulate_idpatterns_odesimulate_idsurveillance_odesimulate_idvaccine_odesimulate_multipathogen_odesimulate_noro_fitsimulate_SEIRSd_model_stochasticsimulate_SIR_model_discretesimulate_SIR_model_odesimulate_SIR_modelexplorationsimulate_SIR_usanalysissimulate_SIRSd_model_odesimulate_SIRSd_model_stochasticsimulate_Vector_transmission_model_ode

Dependencies:adaptivetauaskpassbase64encbslibcachemclicolorspacecommonmarkcpp11crayoncrosstalkcurldata.tabledeSolvedigestdplyrevaluatefansifarverfastmapfontawesomefsgenericsggplot2gluegridExtragtablehighrhtmltoolshtmlwidgetshttpuvhttrisobandjquerylibjsonliteknitrlabelinglaterlatticelazyevallhslifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmenloptropensslpillarpkgconfigplotlypromisespurrrR6rappdirsRColorBrewerRcpprlangrmarkdownsassscalesshinysourcetoolsstringistringrsystibbletidyrtidyselecttinytexutf8vctrsviridisLitewithrxfunXMLxtableyaml

DSAIDE Package Tutorial

Andreas Handel

Rendered fromDSAIDE.Rmdusingknitr::rmarkdownon Sep 12 2024.

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

Readme and manuals

Help Manual

Help pageTopics
The main menu for the DSAIDE packagedsaidemenu
1918 Influenza mortality dataflu1918data
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 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
Cases of norovirus during an outbreaknorodata
A function that runs an app for specific settings and processes results for plot and text generationrun_model
Characteristics of IDsimulate_Characteristics_of_ID_ode
Complex ID Controlsimulate_Complex_ID_Control_ode
Simulation of a compartmental infectious disease transmission model illustrating different types of direct transmissionsimulate_directtransmission_ode
Drug Resistance Evolutionsimulate_Drug_Resistance_Evolution_stochastic
Environmental Transmission modelsimulate_Environmental_Transmission_model_ode
Fitting a SIR-type model to flu datasimulate_flu_fit
Host Heterogeneity Modelsimulate_Host_Heterogeneity_Model_ode
Simulation of a compartmental infectious disease transmission model with 3 types of hosts and interventionsimulate_idcontrolmultigroup_ode
Simulation of a compartmental infectious disease transmission model to study the reproductive numbersimulate_idcontrolmultioutbreak_ode
Simulation of a compartmental infectious disease transmission model including seasonalitysimulate_idpatterns_ode
Simulation of a compartmental infectious disease transmission model illustrating the impact of ID surveillancesimulate_idsurveillance_ode
Simulation of a compartmental infectious disease transmission model to study the reproductive numbersimulate_idvaccine_ode
Simulation of a compartmental infectious disease transmission model with 2 types of pathogenssimulate_multipathogen_ode
Fitting a simple SIR type model to norovirus outbreak datasimulate_noro_fit
SEIRSd modelsimulate_SEIRSd_model_stochastic
SIR modelsimulate_SIR_model_discrete
SIR modelsimulate_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 analysissimulate_SIR_usanalysis
SIRSd modelsimulate_SIRSd_model_ode
SIRSd modelsimulate_SIRSd_model_stochastic
Vector transmission modelsimulate_Vector_transmission_model_ode