Package: swash 2.0.1

swash: Health Geography Toolbox for Model-Based Analysis of Infections Panel Data

Within epidemic outbreaks, infections grow and decline differently between regions, and the velocity of spatial spread differs between countries. The swash library offers a set of model-based analyses for these topics. Spread velocity may be analysed with the Swash-Backwash Model for the Single Epidemic Wave and corresponding functions for bootstrap confidence intervals, country comparison, and visualization of results. Differences in epidemic growth between regions may be analysed using logistic growth models, exponential growth models, Hawkes processes and breakpoint analyses. All functionalities are accessed by the class "infpan" for infections panel data defined in this package, which is built from a data.frame provided by the user.

Authors:Thomas Wieland [aut, cre]

swash_2.0.1.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
swash/json (API)

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

On CRAN:

Conda:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

1.85 score 536 downloads 33 exports 25 dependencies

Last updated from:f767f3e3b2. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK161
source / vignettesOK173
linux-release-x86_64OK168
macos-release-arm64OK157
macos-oldrel-arm64OK196
windows-develOK121
windows-releaseOK117
windows-oldrelOK124
wasm-releaseOK131

Exports:as_balancedbinary_metricsbinary_metrics_glmbreaks_growthcalculate_cumcalculate_incidencecalculate_rollmeancalculate_rollsumcalculate_Rtcompare_countriesconfintexponential_growthgrowthgrowth_breaksgrowth_hawkesgrowth_initialhawkes_growthhist_ciis_balancedload_infections_paneldatalogistic_growthmetricsnbmatrixnbstatplotplot_coef_ciprintquantile_ciR_tsummaryswashswash_backwashtimestamps

Dependencies:bootclassclassIntcpp11DBIdeldire1071genericsKernSmoothlatticelubridateMASSproxyRcpps2sandwichsfspspDataspdepstrucchangetimechangeunitswkzoo

Readme and manuals

Help Manual

Help pageTopics
swash: Health Geography Toolbox for Model-Based Analysis of Infections Panel Dataswash-package
Correction of Non-balanced Panel Dataset with Regional Infection Dataas_balanced
Fit metrics of observed and expected binary variablesbinary_metrics
Fit metrics for binary logit modelbinary_metrics_glm
Time Series Model with Breakpointsbreaks_growth
Class '"breaksgrowth"'breaksgrowth-class plot,breaksgrowth-method print,breaksgrowth-method show,breaksgrowth-method summary,breaksgrowth-method
Regional cumulative COVID-19 deathsC19dNUTSdata
Cumulative Infection Numberscalculate_cum
Methods for Function 'calculate_cum'calculate_cum,infpan-method calculate_cum-methods
Incidence from Infection Numberscalculate_incidence
Methods for Function 'calculate_incidence'calculate_incidence,infpan-method calculate_incidence-methods
Rolling Means of Infection Numberscalculate_rollmean
Methods for Function 'calculate_rollmean'calculate_rollmean,infpan-method calculate_rollmean-methods
Rolling Sums of Infection Numberscalculate_rollsum
Methods for Function 'calculate_rollsum'calculate_rollsum,infpan-method calculate_rollsum-methods
Effective Reproduction Numbercalculate_Rt
Methods for Function 'calculate_Rt'calculate_Rt,infpan-method calculate_Rt-methods
Two-country Comparison of Swash-Backwash Model Parameterscompare_countries
Methods for Function 'confint'confint-methods
Class '"countries"'countries-class plot,countries-method print,countries-method show,countries-method summary,countries-method
Switzerland Daily COVID-19 cases by regionCOVID19Cases_geoRegion
Results from a Difference-in-Differences Modeldid_fatalities_splm_coef
Class '"expgrowth"'expgrowth-class print,expgrowth-method show,expgrowth-method summary,expgrowth-method
Exponential Growth Model for Epidemic Dataexponential_growth
Logistic Growth Models for Regional Infectionsgrowth
Time Series Model with Breakpoints for Regional Infectionsgrowth_breaks
Methods for Function 'growth_breaks'growth_breaks,infpan-method growth_breaks-methods
Hawkes Processs models for Regional Infectionsgrowth_hawkes
Methods for Function 'growth_hawkes'growth_hawkes,infpan-method growth_hawkes-methods
Exponential Growth Models for Regional Infectionsgrowth_initial
Methods for Function 'growth_initial'growth_initial,infpan-method growth_initial-methods
Methods for Function 'growth'growth,infpan-method growth-methods
Class '"growthmodels"'growthmodels-class print,growthmodels-method show,growthmodels-method summary,growthmodels-method
Hawkes Process Model for Epidemic Datahawkes_growth
Class '"hawkes"'hawkes-class plot,hawkes-method print,hawkes-method show,hawkes-method summary,hawkes-method
Creating Histograms with Confidence Intervalshist_ci
InfectionsInfections
Class '"infpan"'infpan-class plot,infpan-method print,infpan-method show,infpan-method summary,infpan-method swash,infpan-method
Test whether Panel Dataset with Regional Infection Data is Balancedis_balanced
Import of infections panel dataload_infections_paneldata
Class '"loggrowth"'loggrowth-class plot,loggrowth-method print,loggrowth-method show,loggrowth-method summary,loggrowth-method
Logistic Growth Model for Epidemic Datalogistic_growth
Fit metrics of observed and expected numeric variablesmetrics
Construct Neighbourhood Matrix from Polygonsnbmatrix
Calculate Neighbourhood Statistics from Polygonsnbstat
Austria Daily COVID-19 cases by region 2020-02-26 to 2020-05-31Oesterreich_Faelle
Plot Point Estimates With Confidence Intervalsplot_coef_ci
Methods for Function 'plot'plot plot,breaksgrowth,ANY-method plot,countries,ANY-method plot,expgrowth,ANY-method plot,hawkes,ANY-method plot,infpan,ANY-method plot,loggrowth,ANY-method plot,sbm,ANY-method plot,sbm_ci,ANY-method
Methods for Function 'print'print-methods
Computing Quantiles for a given Numeric Vectorquantile_ci
Effective Reproduction Number for Epidemic DataR_t
German Counties with COVID-19 CasesRKI_Corona_counties
Class '"sbm_ci"'plot,sbm_ci-method print,sbm_ci-method sbm_ci-class show,sbm_ci-method summary,sbm_ci-method
Class '"sbm"'confint,sbm-method plot,sbm-method print,sbm-method sbm-class show,sbm-method summary,sbm-method
Methods for Function 'show'show-methods
Methods for Function 'summary'summary-methods
Swash-Backwash Model for the Single Epidemic Waveswash
Swash-Backwash Model for the Single Epidemic Waveswash_backwash
Methods for Function 'swash'swash,sbm-method swash-methods
Show timestampstimestamps timestamps,ANY-method