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
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tsiR_0.4.2.tgz(r-4.4-any)tsiR_0.4.2.tgz(r-4.3-any)
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tsiR.pdf |tsiR.html✨
tsiR/json (API)

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

Peer review:

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

Datasets:
  • twentymeas - Measles incidence data from 20 cities

On CRAN:

difference-equationsepidemic-modelepidemicsinfectious-diseasemodel-fittingsir-model

3.56 score 7 stars 26 scripts 226 downloads 4 mentions 29 exports 34 dependencies

Last updated 5 years agofrom:482c550119. Checks:OK: 1 NOTE: 6. Indexed: no.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-winNOTEOct 10 2024
R-4.5-linuxNOTEOct 10 2024
R-4.4-winNOTEOct 10 2024
R-4.4-macNOTEOct 10 2024
R-4.3-winNOTEOct 10 2024
R-4.3-macNOTEOct 10 2024

Exports:corrderivativeepitimesestparsjagsfilterlogcorrmaxthresholdmcmcestparsmcmctsirplotbetaplotbreaksplotcasesplotcompplotdataplotforwardplotLLEplotregressionplotresplotrhoplotsbarpredicttsirresidual.birthsresidual.casesruntsirsimulatetsirTSIR_LETSIR_LLEtsiRdatavplayout

Dependencies:clicolorspacefansifarverggplot2gluegtableisobandkernlablabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigplyrR6RColorBrewerRcppreshape2rlangscalesstringistringrtibbleutf8vctrsviridisLitewithr

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