The task | A run that succeeds | A run that fails, and its retry | What you need to know when you write a task

Setup | A run in one diagram | A plan is one data pull | Analyses iterate within a plan | Only the first and the last plan run in a fixed order | A forked worker MUST NOT inherit an open connection | A task reads cores when it runs | A task builds its plans once per run | A completeness check covers every declared partition | plnr::expand_list() makes one argset per element | Size a plan by its data pull

The two environments | Which variable each backend reads | What check_environment_setup() asks for | Setting the variables from another package | Which one to use

Start here: SQLite, with no server | What SQLite does not need | cs9example needs no .Renviron at all | Which backend to use | 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 | Apache Airflow Integration | Airflow scheduling pattern | Benefits of Airflow + CS9 | Docker Compose with Airflow | Moving from CRAN to full setup | Verification and troubleshooting | Verify your setup | Common issues | Next steps

One rule: every stage takes the ensemble and returns it | A synthetic reporting triangle | 1. Nowcast | 2. Validation: replay the method on the past | The engine completes too much at horizon 0 | 3. Reporting completion: how fast does the data arrive? | What pct_delayD counts | A worked reference week | The weekday of the extract | "As of today", for the weeks on screen | A change in reporting speed: period = "year" | Every number here depends on max_delay_days | 4. Rate: a nowcast numerator over a nowcast denominator | 5. Short-term trend on the rate | Every week gets an interval, the settled weeks too | What that interval is, and what it is not | 6. MEM intensity thresholds | 7. Signal detection: historical limits | 8. Collapse: the end of the chain | 9. Quality control | The naming grammar | Where next

Setup | Per-unit rebuild | Staged import | Per-plan staged swap | Staging as a checkpoint | Fit then fill | Export from a finished table | Notify after export | Three rules

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

Two configurations | The same table against each | What differs | Why the field types are closed | Why the primary key cannot be added later | Which one to choose

What csalert is for | Use the ensemble methods | The current methods work on an ensemble | The deprecated methods work on tables | Where the data formats live | What cannot be done yet | Test data with a known truth

What csutil is for | The seven functions | Two things that surprise people | Where csutil sits | Splitting | Unnesting data frames within a list | Describing lists | Applying a function via hash table

Which year and week is this date? | Get ISO year and ISO week from an ISO yearweek string

What cstime is for | How the function names work | Three things that are easy to get wrong | cstime and the other cs packages | Where to go next | Date to ISO year | ISO yearweek string to ISO year and ISO week | Season week and ISO week

Mapping between ISO week and season week | Conversion functions

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

csfmt_rts_data_v2 | Style | Ordering of variables | Time | Approved events | Location | Ages | Sex | Unified columns | Smart assignment | Context-specific columns | Examples | In action | Expand time to | Time series | Summary | Identifying the data structure of one column | Reference (Location)

What cstidy is for | Which format to use | Three things to know before you move to v3 | v3 derives fewer columns, and removes none | v3 is weekly only | csdb cannot check a v3 table, though it can store one | Where cstidy sits | Where to read next | csfmt_rts_data_v2 | Smart assignment | Summary | Identifying the data structure of one column

Colored maps | Automatic coloring by location_code | Customized coloring with external information | Labeled maps | Enrich plot with additional data | Add county name and population to Norway map | Add location name for ward and population for Oslo map

sf for interactive maps

What csmaps saves you | Choosing a dataset | The three layouts | Two limits worth knowing | How it fits with csdata | Setup | A first map | Where to next

Naming scheme | Scope | Geogranularity | Type | Border | R class | Norway: default | Norway: split | Norway: insert oslo | Oslo ward: default

What csdata is for | Two current limitations | Where csdata sits, and what to read next | Location | Ages | Sex

National trend | Reference tables

What csdb is for | What this vignette does and does not prove | Two classes, and the split between them | The validators, and one gap | The three backends | Where csdb sits | A worked example | Who owns the connection | A connection does not survive a fork | Two tables that declare one index name | Emptying a table before you write to it | The upsert method answers the same four cases

The problem: scaling epidemiological analysis | NorSySS: a decade of operation | CS9 vs alternatives | What is CS9? | When to use CS9 | What CS9 does not decide for you | 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 | What the framework handles for you | Getting started | Next steps

Overview | Themes | Color palettes | Number formatting | Norwegian number format | Date formatting | Norwegian date format | Journal formatting | Number format comparison | Date format comparison | Log scale transformations | Utility functions | Pretty breaks | Every nth label | Further reading

set_csfmt_rts_data_v1