Package: EpiLPS 1.3.0

Oswaldo Gressani

EpiLPS: A Fast and Flexible Bayesian Tool for Estimating Epidemiological Parameters

Estimation of epidemiological parameters with Laplacian-P-splines following the methodology of Gressani et al. (2022) <doi:10.1371/journal.pcbi.1010618>.

Authors:Oswaldo Gressani [aut, cre], Bryan Sumalinab [ctb]

EpiLPS_1.3.0.tar.gz
EpiLPS_1.3.0.tar.gz(r-4.5-noble)EpiLPS_1.3.0.tar.gz(r-4.4-noble)
EpiLPS_1.3.0.tgz(r-4.4-emscripten)EpiLPS_1.3.0.tgz(r-4.3-emscripten)
EpiLPS.pdf |EpiLPS.html✨
EpiLPS/json (API)
NEWS

# Install 'EpiLPS' in R:

install.packages('EpiLPS', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/oswaldogressani/epilps/issues

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3
openmp– GCC OpenMP (GOMP) support library

Datasets:

cov19incidence2022 - Incidence data for Belgium in 2022
cov19mort2021 - Mortality data for Belgium in 2021
eruptions - Eruption times in Yellowstone National Park
influenza2009 - Data on the 2009 pandemic influenza in Pennsylvania
sars2003 - Daily incidence of the 2003 SARS epidemic in Hong Kong
zika2015 - Data on the 2015 Zika virus disease in Colombia

2.78 score 1 stars 12 scripts 331 downloads 12 exports 47 dependencies

Last updated 8 months agofrom:6899f2b6aa. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 05 2024
R-4.5-linux-x86_64	OK	Oct 05 2024

Exports:epicurve episim estimIncub estimR estimRmcmc histosmooth Idist incubsim nowcasting nowcastingR perfRestim Rmodelpriors

Dependencies:aweek cli coarseDataTools coda colorspace EpiEstim fansi farver fitdistrplus ggplot2 glue gridExtra gtable incidence isoband labeling lattice lifecycle magrittr MASS Matrix MatrixModels mcmc MCMCpack mgcv munsell nlme pillar pkgconfig plyr quantreg R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang scales SparseM stringi stringr survival tibble utf8 vctrs viridisLite withr

Reproduction number

Oswaldo Gressani

Rendered fromReproduction-number.Rmdusingknitr::rmarkdownon Oct 05 2024.

Last update: 2023-08-30
Started: 2023-08-30

Citation

Readme and manuals

Help Manual

Help page	Topics
Incidence data for Belgium in 2022	cov19incidence2022
Mortality data for Belgium in 2021	cov19mort2021
Plot the epidemic curve	epicurve
Simulation of an incidence time series	episim
Eruption times in Yellowstone National Park	eruptions
Estimation of the incubation density based on coarse data	estimIncub
Estimation of the reproduction number with Laplacian-P-splines	estimR
Estimation of the reproduction number with Laplacian-P-splines via MCMC	estimRmcmc
Histogram smoothing with Laplacian-P-splines	histosmooth
Density function and discrete distribution for a disease interval	Idist
Simulation of incubation times	incubsim
Data on the 2009 pandemic influenza in Pennsylvania	influenza2009
Nowcasting and estimation of occurred but not yet reported events	nowcasting
Nowcasting the reproduction number	nowcastingR
Routine to measure the performance of estimR and estimRmcmc	perfRestim
Plot the interval distribution from an Idist object	plot.Idist
Plot the estimated incubation distribution	plot.incubestim
Plot of nowcasted cases and delay distribution	plot.nowcasted
Plot the estimated reproduction number	plot.Rt
Plot the nowcasted reproduction number	plot.Rtnow
Prior specification for model hyperparameters	Rmodelpriors
Daily incidence of the 2003 SARS epidemic in Hong Kong	sars2003
Summarize the estimated reproduction number	summary.Rt
Data on the 2015 Zika virus disease in Colombia	zika2015