Package: EpiLPS 1.4.0

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_1.4.0.tar.gz
EpiLPS_1.4.0.zip(r-4.5)EpiLPS_1.4.0.zip(r-4.4)EpiLPS_1.4.0.zip(r-4.3)
EpiLPS_1.4.0.tgz(r-4.4-x86_64)EpiLPS_1.4.0.tgz(r-4.4-arm64)EpiLPS_1.4.0.tgz(r-4.3-x86_64)EpiLPS_1.4.0.tgz(r-4.3-arm64)
EpiLPS_1.4.0.tar.gz(r-4.5-noble)EpiLPS_1.4.0.tar.gz(r-4.4-noble)
EpiLPS_1.4.0.tgz(r-4.4-emscripten)EpiLPS_1.4.0.tgz(r-4.3-emscripten)
EpiLPS.pdf |EpiLPS.html✨
EpiLPS/json (API)
NEWS

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

Peer review:

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:

On CRAN:

4.66 score 19 stars 12 scripts 311 downloads 13 exports 47 dependencies

Last updated 30 days agofrom:9a8b938f7e. Checks:OK: 6 NOTE: 3. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 23 2024
R-4.5-win-x86_64OKNov 23 2024
R-4.5-linux-x86_64OKNov 23 2024
R-4.4-win-x86_64NOTENov 23 2024
R-4.4-mac-x86_64NOTENov 23 2024
R-4.4-mac-aarch64NOTENov 23 2024
R-4.3-win-x86_64OKNov 23 2024
R-4.3-mac-x86_64OKNov 23 2024
R-4.3-mac-aarch64OKNov 23 2024

Exports:epicurveepisimestimIncubestimRestimRmcmcestimSIhistosmoothIdistincubsimnowcastingnowcastingRperfRestimRmodelpriors

Dependencies:aweekclicoarseDataToolscodacolorspaceEpiEstimfansifarverfitdistrplusggplot2gluegridExtragtableincidenceisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixModelsmcmcMCMCpackmgcvmunsellnlmepillarpkgconfigplyrquantregR6RColorBrewerRcppRcppArmadilloreshape2rlangscalesSparseMstringistringrsurvivaltibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Incidence data for Belgium in 2022cov19incidence2022
Mortality data for Belgium in 2021cov19mort2021
Plot the epidemic curveepicurve
Simulation of an incidence time seriesepisim
Eruption times in Yellowstone National Parkeruptions
Estimation of the incubation density based on coarse dataestimIncub
Estimation of the reproduction number with Laplacian-P-splinesestimR
Estimation of the reproduction number with Laplacian-P-splines via MCMCestimRmcmc
Nonparametric serial interval estimationestimSI
Histogram smoothing with Laplacian-P-splineshistosmooth
Density function and discrete distribution for a disease intervalIdist
Simulation of incubation timesincubsim
Data on the 2009 pandemic influenza in Pennsylvaniainfluenza2009
Serial interval data for the 2009 outbreak of pandemic Influenza A (H1N1)influenza2009serial
Nowcasting and estimation of occurred but not yet reported eventsnowcasting
Nowcasting the reproduction numbernowcastingR
Routine to measure the performance of estimR and estimRmcmcperfRestim
Plot the interval distribution from an Idist objectplot.Idist
Plot the estimated incubation distributionplot.incubestim
Plot of nowcasted cases and delay distributionplot.nowcasted
Plot the estimated reproduction numberplot.Rt
Plot the nowcasted reproduction numberplot.Rtnow
Prior specification for model hyperparametersRmodelpriors
Daily incidence of the 2003 SARS epidemic in Hong Kongsars2003
Summarize the estimated reproduction numbersummary.Rt
Data on the 2015 Zika virus disease in Colombiazika2015