Package: tsiR 0.4.2

Alexander D. Becker

tsiR: An Implementation of the TSIR Model

An implementation of the time-series Susceptible-Infected-Recovered (TSIR) model using a number of different fitting options for infectious disease time series data. The manuscript based on this package can be found here <https://doi:10.1371/0185528>. The method implemented here is described by Finkenstadt and Grenfell (2000) <doi:10.1111/1467-9876.00187>.

Authors:Alexander D. Becker [aut, cre], Sinead E. Morris [ctb], Ottar N. Bjornstad [ctb]

tsiR_0.4.2.tar.gz
tsiR_0.4.2.zip(r-4.7-any)tsiR_0.4.2.zip(r-4.6-any)tsiR_0.4.2.zip(r-4.5-any)
tsiR_0.4.2.tgz(r-4.6-any)tsiR_0.4.2.tgz(r-4.5-any)
tsiR_0.4.2.tar.gz(r-4.7-any)tsiR_0.4.2.tar.gz(r-4.6-any)
tsiR_0.4.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
tsiR/json (API)

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

Bug tracker:https://github.com/adbecker/tsir/issues

Datasets:
  • twentymeas - Measles incidence data from 20 cities

On CRAN:

Conda:

difference-equationsepidemic-modelepidemicsinfectious-diseasemodel-fittingsir-model

3.70 score 9 stars 28 scripts 283 downloads 4 mentions 29 exports 24 dependencies

Last updated from:482c550119. Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-develNOTE126
source / vignettesOK151
linux-releaseNOTE142
macos-releaseNOTE108
macos-oldrelNOTE120
windows-develNOTE85
windows-releaseNOTE83
windows-oldrelNOTE94
wasm-releaseOK111

Exports:corrderivativeepitimesestparsjagsfilterlogcorrmaxthresholdmcmcestparsmcmctsirplotbetaplotbreaksplotcasesplotcompplotdataplotforwardplotLLEplotregressionplotresplotrhoplotsbarpredicttsirresidual.birthsresidual.casesruntsirsimulatetsirTSIR_LETSIR_LLEtsiRdatavplayout

Dependencies:clicpp11farverggplot2gluegtableisobandkernlablabelinglifecyclemagrittrplyrR6RColorBrewerRcppreshape2rlangS7scalesstringistringrvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
corrcorr
derivativederivative
epitimesepitimes
estparsestpars
jagsfilterjagsfilter
logcorrlogcorr
maxthresholdmaxthreshold
mcmcestparsmcmcestpars
mcmctsirmcmctsir
plotbetaplotbeta
plotbreaksplotbreaks
plotcasesplotcases
plotcompplotcomp
plotdataplotdata
plotforwardplotforward
plotLLEplotLLE
plotregressionplotregression
plotresplotres
plotrhoplotrho
plotsbarplotsbar
predicttsirpredicttsir
residuals.birthsresidual.births
residuals.casesresidual.cases
runtsirruntsir
simulatetsirsimulatetsir
TSIR_LETSIR_LE
TSIR_LLETSIR_LLE
tsiRdatatsiRdata
Measles incidence data from 20 citiestwentymeas
vplayoutvplayout