Package: ViroReportR 1.0.5

Mike Irvine

ViroReportR: Respiratory Viral Infection Forecast Reporting

Tools for reporting and forecasting viral respiratory infections, using case surveillance data. Report generation tools for short-term forecasts, and validation metrics for an arbitrary number of customizable respiratory viruses. Estimation of the effective reproduction number is based on the 'EpiEstim' framework described in work by 'Cori' and colleagues. (2013) <doi:10.1093/aje/kwt133>.

Authors:Mike Irvine [aut, cre, cph], Caesar Wong [aut], Nirupama Tamvada [aut], Rebeca Falcao [aut], Nelson Tang [aut]

ViroReportR_1.0.5.tar.gz
ViroReportR_1.0.5.zip(r-4.7-any)ViroReportR_1.0.5.zip(r-4.6-any)ViroReportR_1.0.5.zip(r-4.5-any)
ViroReportR_1.0.5.tgz(r-4.6-any)ViroReportR_1.0.5.tgz(r-4.5-any)
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ViroReportR_1.0.5.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ViroReportR/json (API)

# Install 'ViroReportR' in R:

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

Bug tracker:https://github.com/bccdc-phsa/viroreportr/issues

Pkgdown/docs site:https://bccdc-phsa.github.io

On CRAN:

5.68 score 2 stars 8 scripts 355 downloads 8 exports 82 dependencies

Last updated from:0ff822fcb0. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	180
source / vignettes	OK	208
linux-release	OK	177
macos-release	OK	221
macos-oldrel	OK	204
windows-devel	OK	130
windows-release	OK	134
windows-oldrel	OK	121
wasm-release	OK	119

Exports:generate_forecast generate_forecast_report generate_validation generate_validation_metric get_aggregated_data plot_rt plot_validation simulate_data

Dependencies:aweek base64enc bslib cachem cli coarseDataTools coda cowplot cpp11 data.table digest dplyr EpiEstim evaluate farver fastmap fitdistrplus fontawesome fs generics ggplot2 glue gridExtra gtable highr htmltools incidence isoband jquerylib jsonlite kableExtra knitr labeling lattice lifecycle lubridate magrittr MASS Matrix MatrixModels mcmc MCMCpack memoise mgcv mime nlme pillar pkgconfig plyr projections purrr quantreg R6 rappdirs RColorBrewer Rcpp reshape2 rlang rmarkdown rstudioapi S7 sass scales SparseM stringi stringr survival svglite systemfonts textshaping tibble tidyr tidyselect timechange tinytex utf8 vctrs viridisLite withr xfun xml2 yaml

Model fitting and producing short-term forecasts using daily data with EpiEstim

Overview | Loading data | Model fitting and forecasting | Validation | Forecast Report

Rendered fromvriforecasting-model-fitting-epiestim.Rmdusingknitr::rmarkdown

Last update: 2026-02-17
Started: 2024-02-13

Help page	Topics
Clean and validate case count data for EpiEstim	clean_sample_data
summarise a data frame 'd' by groups along a 'variable'	create_quantiles
Print out text output for ViroReportR report detailing current number of case visits, last value of Rt and corresponding intervals	current_forecast_text
fit_epiestim_model - Function to estimate the reproduction number of an epidemic	fit_epiestim_model
Extract current forecast metrics: forecast prediction, percentile interval and Rt value	forecast_metrics
Forecast daily epidemic cases using EpiEstim	generate_forecast
Generate Viral Respiratory Forecast Report	generate_forecast_report
Validate forecast performance over multiple time windows	generate_validation
Compute Forecast Validation Metrics (SMAPE & MASE)	generate_validation_metric
Extract Aggregated Weekly Generic Data	get_aggregated_data
Plot Mean Rt with time index (dates)	plot_rt
Plot a ribbon plot with each time horizon predictions against true values for validation	plot_validation
Extract daily forecast samples	project_epiestim_model
Simulate Daily Virus Incidence Data	simulate_data

Package: ViroReportR 1.0.5

ViroReportR: Respiratory Viral Infection Forecast Reporting

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Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)