Package: cs9 26.5.13

Richard Aubrey White

cs9: A Framework for Real-Time Analysis and Disease Surveillance

A comprehensive framework for building real-time disease surveillance systems. Provides R6-based infrastructure for database-driven surveillance tasks, with support for parallel processing, data validation, and automated pipeline execution. Designed for epidemiological analysis and public health monitoring applications.

Authors:Richard Aubrey White [aut, cre], Core Surveillance [cph]

cs9_26.5.13.tar.gz
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cs9_26.5.13.tgz(r-4.6-any)cs9_26.5.13.tgz(r-4.5-any)
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cs9_26.5.13.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
cs9/json (API)

# Install 'cs9' in R:
install.packages('cs9', repos = c('https://niphr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/niphr/cs9/issues

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

On CRAN:

Conda:

4.00 score 3 scripts 16 exports 78 dependencies

Last updated from:25d11d919b. Checks:7 NOTE, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64NOTE161
source / vignettesOK215
linux-release-x86_64NOTE196
macos-release-arm64NOTE148
macos-oldrel-arm64NOTE100
windows-develNOTE93
windows-releaseNOTE89
windows-oldrelNOTE96
wasm-releaseOK169

Exports:%>%check_environment_setupconfigcreate_folder_if_doesnt_existcreate_latest_folderget_config_data_hash_for_each_planget_config_logget_config_tables_last_updatedget_config_tasks_statsmandatory_db_filterpathrun_task_sequentially_as_callr_bg_using_load_allrun_task_sequentially_as_rstudio_job_using_load_allSurveillanceSystem_v9TaskJobupdate_config_log

Dependencies:askpassbitbit64blobcallrclicliprcodetoolscpp11crayoncredentialscsdbcstimecsutilcurldata.tableDBIdescdigestdplyrfarverforeachfsgenericsgertggplot2gitcredsgluegtablehmshttr2iniisobanditeratorsjsonlitelabelinglaterlifecyclelubridatemagrittrodbcopensslotelpbmcapplypillarpkgconfigplnrprettyunitsprocessxprogressprogressrpspurrrR6rappdirsRColorBrewerRcpprlangrprojrootrstudioapiS7scalesstringistringrsystibbletidyrtidyselecttimechangeusethisutf8uuidvctrsviridisLitewhiskerwithryamlzip

Creating a task
Overview | Prerequisites | Step 1: Initialize a surveillance system | Step 2: Define database tables | Step 3: Implement task functions | Data selector function | Action function | Step 4: Configure the task | Step 5: Execute the task | Step 6: Monitor and debug tasks | Advanced task features | Parallel processing | Dynamic plan generation | Best practices | Error handling | Data validation | Modular design | Summary | See also
Rendered fromcreating-a-task.Rmdusingknitr::rmarkdown

Last update: 2026-06-30
Started: 2025-08-20

File Layout
Starting from the example package | 00_env_and_namespace.R | 01_definitions.R | 02_surveillance_systems.R | 03_tables.R | 04_tasks.R | 05_deliverables.R | 10_onLoad.R | 11_onAttach.R | Task files | weather_download_and_import_rawdata.R | weather_clean_data.R | weather_export_weather_plots.R | Notes | Next steps
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Last update: 2026-06-30
Started: 2023-03-09

Installation
Installation options | CRAN installation (limited functionality) | Full installation (database-driven surveillance) | Database setup | PostgreSQL installation | Option 1: Docker (recommended) | Option 2: System installation | Database schema setup | Environment variable configuration | Setting up .Renviron | Variable descriptions | Package behavior without database configuration | Docker | Moving from CRAN to full setup | Verification and troubleshooting | Verify your setup | Common issues | Next steps
Rendered frominstallation.Rmdusingknitr::rmarkdown

Last update: 2026-06-30
Started: 2023-03-07

Introduction to CS9
What is CS9? | When to use CS9 | Key concepts and definitions | Surveillance system architecture | Example workflow | Plan-heavy or analysis-heavy tasks? | Other vignettes | Example | Surveillance system setup | Database table definition | Task configuration | for_each_plan | plnr::expand_list | for_each_analysis | universal_argset | upsert_at_end_of_each_plan | insert_at_end_of_each_plan | action_fn_name | data_selector_fn_name | schema | data_selector_fn | action_fn | Run the task | Common task patterns | Importing data | Analysis | Exporting multiple sets of results | Exporting combined results | Deployment | Getting started | Next steps
Rendered fromcs9.Rmdusingknitr::rmarkdown

Last update: 2026-06-30
Started: 2024-05-27