Package: csalert 2026.7.1

Richard Aubrey White

csalert: Alerts from Public Health Surveillance Data

Helps create alerts and determine trends by using various methods to analyze public health surveillance data. The primary analysis method is based upon a published analytics strategy by Benedetti (2019) <doi:10.5588/pha.19.0002>.

Authors:Beatriz Valcarcel Salamanca [aut], Chi Zhang [aut], Richard Aubrey White [aut, cre]

csalert_2026.7.1.tar.gz
csalert_2026.7.1.zip(r-4.7)csalert_2026.7.1.zip(r-4.6)csalert_2026.7.1.zip(r-4.5)
csalert_2026.7.1.tgz(r-4.6-any)csalert_2026.7.1.tgz(r-4.5-any)
csalert_2026.7.1.tar.gz(r-4.7-any)csalert_2026.7.1.tar.gz(r-4.6-any)
csalert_2026.7.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
csalert/json (API)

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

Bug tracker:https://github.com/niphr/csalert/issues

Pkgdown/docs site:https://niphr.github.io

On CRAN:

Conda:

csverse

3.78 score 1 stars 687 downloads 32 exports 45 dependencies

Last updated from:d481348e30. Checks:7 NOTE, 2 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE190
source / vignettesOK246
linux-release-x86_64NOTE166
macos-release-arm64NOTE137
macos-oldrel-arm64NOTE118
windows-develNOTE170
windows-releaseNOTE144
windows-oldrelNOTE264
wasm-releaseOK175

Exports:add_holiday_effectcompare_resultscsfmt_ensemble_v3csfmt_interpretcsfmt_parsecsfmt_reporting_triangle_v3csfmt_varens_add_rateens_collapsemem_thresholds_v1nowcast_backtestnowcast_censornowcast_evaluate_v1nowcast_passthrough_to_ensemble_v1nowcast_quasipoisson_v1nowcast_truthq_labelq_valueqc_surveillance_dataqc_week_over_weekreporting_completionreporting_completion_trend_v1reporting_triangle_matrixrolling_slope_matrixset_time_series_idshort_term_trendshort_term_trend_sts_v1signal_detection_hlmsimulate_baseline_datasimulate_seasonal_outbreak_datasimulate_spike_outbreak_datavalidate_ensemble

Dependencies:clicpp11crayoncsdatacstidycstimedata.tabledeldirdigestfarvergenericsggplot2glm2gluegtableisobandlabelinglatticelifecyclelubridatemagrittrMASSMatrixmatrixStatsnlmepolyclippolyCubR6RColorBrewerrlangS7scalesspspatstat.dataspatstat.geomspatstat.univarspatstat.utilsstringistringrsurveillancetimechangevctrsviridisLitewithrxtable

Nowcasting a reporting triangle with csfmt_ensemble_v3
A synthetic reporting triangle | Nowcasting | Is the nowcast any good? A replay backtest | How fast does the data arrive? Reporting completion | The naming grammar | Where next
Rendered fromnowcasting.Rmdusingknitr::rmarkdown

Last update: 2026-07-02
Started: 2026-07-02

Short term trend
Single location | Covid-19 hospitalisation data | Data in cstidy format | Weekly observations | Visualising trend status | Multiple locations | Mapping trend status
Rendered fromshort_term_trend.Rmdusingknitr::rmarkdown

Last update: 2026-06-30
Started: 2022-04-20

Readme and manuals

Help Manual

Help pageTopics
Apply a public holiday effect to simulated dataadd_holiday_effect
Compare two collapsed csfmt result setscompare_results
Construct a csfmt_ensemble_v3csfmt_ensemble_v3
Interpret a dataset's columns via the naming grammarcsfmt_interpret
Parse a csfmt measure column name into components (inverse of [csfmt_var])csfmt_parse
Construct a csfmt_reporting_triangle_v3csfmt_reporting_triangle_v3
Construct a csfmt measure column name from componentscsfmt_var
Add a rate measure to an ensembleens_add_rate ens_add_rate.csfmt_ensemble_v3
Collapse a csfmt_ensemble_v3 to a quantile-summaryens_collapse ens_collapse.csfmt_ensemble_v3
MEM intensity thresholdsmem_thresholds_v1 mem_thresholds_v1.csfmt_ensemble_v3
Replay a nowcast method across as-of weeks (backtest)nowcast_backtest
Censor a reporting triangle to what was known "as of" a past weeknowcast_censor
Evaluate nowcast method(s): interval coverage + point-estimate revisionnowcast_evaluate_v1
Build an ensemble from a reporting triangle WITHOUT nowcasting (passthrough)nowcast_passthrough_to_ensemble_v1
Nowcast a reporting triangle into an ensemble (quasipoisson reporting regression)nowcast_quasipoisson_v1 nowcast_quasipoisson_v1.csfmt_reporting_triangle_v3
The settled (eventually-observed) total per reference weeknowcast_truth
Prediction thresholdsprediction_interval
Prediction thresholdsprediction_interval.glm
Print a `csfmt_ensemble_v3`print.csfmt_ensemble_v3
Probability -> controlled-vocabulary quantile labelq_label
Quantile label -> probability (inverse of [q_label])q_value
Quality-control checks on surveillance input dataqc_surveillance_data
Week-over-week QC: settled-data integrity (A) + frontier status signal (B)qc_week_over_week
Empirical reporting-completion summary from a reporting trianglereporting_completion
Reporting-completion trend: the delay curve by year and recent monthsreporting_completion_trend_v1
Densify a reporting triangle into per-series reference x delay count matricesreporting_triangle_matrix
Rolling OLS slope over a weeks x draws matrixrolling_slope_matrix
Assign content-hash time_series_id (+ readable label) by referenceset_time_series_id
Determine the short term trend of a timeseriesshort_term_trend short_term_trend.csfmt_ensemble_v3 short_term_trend.csfmt_rts_data_v1
Determine the short term trend of a surveillance time seriesshort_term_trend_sts_v1
Detect signals using the historical limits methodsignal_detection_hlm signal_detection_hlm.csfmt_ensemble_v3 signal_detection_hlm.csfmt_rts_data_v1
Simulate baseline surveillance datasimulate_baseline_data
Add seasonal outbreaks to simulated datasimulate_seasonal_outbreak_data
Add spiked outbreaks to simulated datasimulate_spike_outbreak_data
Validate a csfmt_ensemble_v3's invariantsvalidate_ensemble