Package: swash 3.0.3

Thomas Wieland

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 of the Single Epidemic Wave by Cliff and Haggett (2006) <doi:10.1007/s10109-006-0027-8> 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. Cluster and hotspot analyses can be conducted using neighborhood matrices. See Wieland (2020) <doi:10.18335/region.v7i2.324> for an application of some of the mentioned analysis methods. 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_3.0.3.tar.gz
swash_3.0.3.zip(r-4.7-any)swash_3.0.3.zip(r-4.6-any)
swash_3.0.3.tar.gz(r-4.7-any)swash_3.0.3.tar.gz(r-4.6-any)
swash_3.0.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
swash/json (API)

# Install 'swash' in R:
install.packages('swash', repos = c('https://cran.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.

2.04 score 4 scripts 682 downloads 39 exports 27 dependencies

Last updated from:7d428a51fb. Checks:6 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develOK165
source / vignettesOK170
linux-releaseOK156
windows-develOK116
windows-releaseOK107
wasm-releaseOK108

Exports:add_geodataas_balancedbinary_metricsbinary_metrics_glmbreaks_growthcalculate_cumcalculate_incidencecalculate_rollmeancalculate_rollsumcalculate_Rtcompare_countriesconfintexponential_growthgetisordgrowthgrowth_breaksgrowth_hawkesgrowth_initialgstarhawkes_growthhist_ciis_balancedload_infections_paneldatalogistic_growthmetricsmorannbmatrixnbstatplotplot_coef_ciplot_mapprintquantile_ciR_tspatial_statisticsummaryswashswash_backwashtimestamps

Dependencies:bootclassclassIntclicpp11DBIdeldire1071genericsKernSmoothlatticelubridateproxyRcpprlangs2sandwichsfsfdepspspDataspdepstrucchangetimechangeunitswkzoo

Readme and manuals

Help Manual

Help pageTopics
swash: Health Geography Toolbox for Model-Based Analysis of Infections Panel Dataswash-package
Adding Geodata to Infpan Objectadd_geodata
Methods for Function 'add_geodata'add_geodata,infpan-method add_geodata-methods
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
Calculate Global Getis-Ord statisticgetisord
Methods for Function 'getisord'getisord,nbmatrix-method getisord-methods
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 Process 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
Calculate Local Getis-Ord Gi* statisticgstar
Methods for Function 'gstar'gstar,nbmatrix-method gstar-methods
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
Swiss Canton BoundariesK4kant20260101gf_ch2007Poly
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
Calculate Global Moran's I statisticmoran
Methods for Function 'moran'moran,nbmatrix-method moran-methods
Construct Neighbourhood Matrix from Polygonsnbmatrix
Class '"nbmatrix"'nbmatrix-class nbstat,nbmatrix-method plot,nbmatrix-method print,nbmatrix-method show,nbmatrix-method summary,nbmatrix-method
Calculate Neighbourhood Statistics from Polygonsnbstat
Methods for Function 'nbstat'nbstat,infpan-method nbstat-methods
Austria Daily COVID-19 cases by region 2020-02-26 to 2020-05-31Oesterreich_Faelle
Plot Point Estimates With Confidence Intervalsplot_coef_ci
Map Plot of Specified Indicatorplot_map
Methods for Function 'plot_map'plot_map,infpan-method plot_map-methods
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,nbmatrix,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
Calculating Spatial Statisticsspatial_statistic
Methods for Function 'spatial_statistic'spatial_statistic,infpan-method spatial_statistic-methods
Methods for Function 'summary'summary-methods
Swash-Backwash Model of the Single Epidemic Waveswash
Swash-Backwash Model of the Single Epidemic Waveswash_backwash
Methods for Function 'swash'swash,sbm-method swash-methods
Show timestampstimestamps timestamps,ANY-method