This package is considered a duplicate. The official version of this package is found at:https://adbecker.r-universe.dev/tsiR

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-4.5)tsiR_0.4.2.zip(r-4.4)tsiR_0.4.2.zip(r-4.3)
tsiR_0.4.2.tgz(r-4.4-any)tsiR_0.4.2.tgz(r-4.3-any)
tsiR_0.4.2.tar.gz(r-4.5-noble)tsiR_0.4.2.tar.gz(r-4.4-noble)
tsiR_0.4.2.tgz(r-4.4-emscripten)tsiR_0.4.2.tgz(r-4.3-emscripten)
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'))

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

Datasets:

twentymeas - Measles incidence data from 20 cities

On CRAN:

difference-equations epidemic-model epidemics infectious-disease model-fitting sir-model

3.56 score 7 stars 26 scripts 225 downloads 4 mentions 29 exports 34 dependencies

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

Target	Result	Date
Doc / Vignettes	OK	Nov 09 2024
R-4.5-win	NOTE	Nov 09 2024
R-4.5-linux	NOTE	Nov 09 2024
R-4.4-win	NOTE	Nov 09 2024
R-4.4-mac	NOTE	Nov 09 2024
R-4.3-win	NOTE	Nov 09 2024
R-4.3-mac	NOTE	Nov 09 2024

Exports:corr derivative epitimes estpars jagsfilter logcorr maxthreshold mcmcestpars mcmctsir plotbeta plotbreaks plotcases plotcomp plotdata plotforward plotLLE plotregression plotres plotrho plotsbar predicttsir residual.births residual.cases runtsir simulatetsir TSIR_LE TSIR_LLE tsiRdata vplayout

Dependencies:cli colorspace fansi farver ggplot2 glue gtable isoband kernlab labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig plyr R6 RColorBrewer Rcpp reshape2 rlang scales stringi stringr tibble utf8 vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
corr	corr
derivative	derivative
epitimes	epitimes
estpars	estpars
jagsfilter	jagsfilter
logcorr	logcorr
maxthreshold	maxthreshold
mcmcestpars	mcmcestpars
mcmctsir	mcmctsir
plotbeta	plotbeta
plotbreaks	plotbreaks
plotcases	plotcases
plotcomp	plotcomp
plotdata	plotdata
plotforward	plotforward
plotLLE	plotLLE
plotregression	plotregression
plotres	plotres
plotrho	plotrho
plotsbar	plotsbar
predicttsir	predicttsir
residuals.births	residual.births
residuals.cases	residual.cases
runtsir	runtsir
simulatetsir	simulatetsir
TSIR_LE	TSIR_LE
TSIR_LLE	TSIR_LLE
tsiRdata	tsiRdata
Measles incidence data from 20 cities	twentymeas
vplayout	vplayout