diff --git a/docs/api/rvdss.md b/docs/api/rvdss.md new file mode 100644 index 000000000..c5a661db0 --- /dev/null +++ b/docs/api/rvdss.md @@ -0,0 +1,189 @@ +--- +title: Respiratory Virus Detections in Canada +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 1 +--- + +# Respiratory Virus Detections in Canada + +{: .no_toc} + +- **Source name:** `rvdss` +- **Earliest issue available:** Epiweek 36 2013 (2013-09-07) +- **Date of last change:** Never +- **Available for:** province, lab, region, nation (see [Geography](#geography)) +- **Time type:** week (see [date format docs](../covidcast_times.md)) +- **License:** **Open Government Licence - Canada** + +This data source of respiratory virus detections in Canada is collected by the [Respiratory Virus Detection Surveillance System](https://health-infobase.canada.ca/respiratory-virus-surveillance/?source=rvdss) (RVDSS) and published by the Public Health Agency of Canada (PHAC). Laboratory tests for various respiratory illnesses from various sentinel laboratories across Canada are reported on a weekly basis year-round to the [Centre for Immunization and Respiratory Infectious Diseases (CIRID)](https://www.canada.ca/en/public-health/services/infectious-diseases/centre-immunization-respiratory-infectious-diseases-cirid.html), Public Health Agency of Canada. The data was originally scraped when weekly online reports, but since June 2024, has been reported on a dynamic dashboard. + +NOTE: Pandemic COVID-19 is not reported in this data source. + +| Signal | Description | +|---------------------|---------------------------------------------------| +| `sarscov2_tests` | Number of SARS-CoV-2 laboratory tests
**Earliest Date Available:** 2022-09-03 | +| `sarscov2_positive_tests` | Number of Positive SARS-CoV-2 laboratory tests
**Earliest Date Available:** 2022-09-03 | +| `sarscov2_pct_positive` | Percentage of SARS-CoV-2 laboratory tests that are positive
**Earliest Date Available:** 2022-09-03 | +| `flu_tests` | Number of Influenza laboratory tests (for all subtypes)
**Earliest Date Available:** 2013-08-31 | +| `flua_tests` | Number of Influenza A laboratory tests (Same as `flu_tests`, just maintained for convenience)
**Earliest Date Available:** 2013-08-31 | +| `flub_tests` | Number of Influenza B laboratory tests (Same as `flu_tests`, just maintained for convenience)
**Earliest Date Available:** 2013-08-31 | +| `flu_positive_tests` | Number of positive Influenza laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `flu_pct_positive` | Percentage of Influenza laboratory tests that are positive (for all subtypes)
**Earliest Date Available:** 2013-08-31 | +| `fluah1n1pdm09_positive_tests` | Number of positive Influenza A(H1N1)pdm09 laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `fluah3_positive_tests` | Number of positive Influenza A(H3N2) laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `fluauns_positive_tests` | Number of positive Influenza A (Unsubtyped)laboratory tests
**Earliest Date Available:** 2016-09-03 | +| `flua_positive_tests` | Number of positive Influenza A laboratory tests (for all subtypes)
**Earliest Date Available:** 2013-08-31 | +| `flua_pct_positive` | Percentage of Influenza A laboratory tests that are positive (for all subtypes)
**Earliest Date Available:** 2013-08-31 | +| `flub_positive_tests` | Number of positive Influenza B laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `flub_pct_positive` | Percentage of Influenza B laboratory tests that are positive
**Earliest Date Available:** 2013-08-31 | +| `rsv_tests` | Number of Respiratory Syncytial Virus (RSV) laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `rsv_positive_tests` | Number of positive RSV laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `rsv_pct_positive` | Percentage of RSV laboratory tests that are positive
**Earliest Date Available:** 2013-08-31 | +| `hpiv_tests` | Number of Human Parainfluenza Virus (HPIV) laboratory tests (for all subtypes)
**Earliest Date Available:** 2013-08-31 | +| `hpiv1_positive_tests` | Number of positive HPIV-1 laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `hpiv2_positive_tests` | Number of positive HPIV-2 laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `hpiv3_positive_tests` | Number of positive HPIV-3 laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `hpiv4_positive_tests` | Number of positive HPIV-4 laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `hpivother_positive_tests` | Number of positive other HPIV laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `hpiv_positive_tests` | Number of positive HPIV laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `hpiv_pct_positive` | Percentage of HPIV laboratory tests that are positive (for all subtypes)
**Earliest Date Available:** 2013-08-31 | +| `adv_tests` | Number of Adenovirus (ADV) laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `adv_positive_tests` | Number of positive ADV laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `adv_pct_positive` | Percentage of ADV laboratory tests that are positive
**Earliest Date Available:** 2013-08-31 | +| `hmpv_tests` | Number of Human Metapneumovirus (hMPV)laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `hmpv_positive_tests` | Number of positive hMPV laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `hmpv_pct_positive` | Percentage of hMPV laboratory tests that are positive
**Earliest Date Available:** 2013-08-31 | +| `evrv_tests` | Number of Enterovirus/Rhinovirus (EV/RV) laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `evrv_positive_tests` | Number of positive EV/RV laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `evrv_pct_positive` | Percentage of EV/RV laboratory tests that are positive
**Earliest Date Available:** 2013-08-31 | +| `hcov_tests` | Number of Human Coronavirus (HCoV) laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `hcov_positive_tests` | Number of positive HCoV laboratory tests
**Earliest Date Available:** 2013-08-31 | +| `hcov_pct_positive` | Percentage of HCoV laboratory tests that are positive
**Earliest Date Available:** 2013-08-31 | +| `week` | Current epidemiological week number
**Earliest Date Available:** 2023-09-02 | +| `weekorder` | Week number in the current season
**Earliest Date Available:** 2023-09-02 | +| `year` | Current year
**Earliest Date Available:** 2023-09-02 | +| `region` | Region the `geo_value` (see [Geography](#geography))
**Earliest Date Available:** 2023-09-02 | + +## Table of contents + +{: .no_toc .text-delta} + +1. TOC {:toc} + +## Geography {#geography} + +Unlike most other sources in the Delphi Epidata API, this data source is Canadian. The `geo_value` argument specifies which geographic level to get data for, and accepts the following: + +**`province`**: One of the 10 provinces or three territories, abbreviated using [internationally approved 2-letter alpha codes](https://www.canada.ca/en/government/system/digital-government/digital-government-innovations/enabling-interoperability/gc-enterprise-data-reference-standards/data-reference-standard-canadian-provinces-territories.html) + +- `nl`: Newfoundland and Labrador + +- `pe`: Prince Edward Island + +- `ns`: Nova Scotia + +- `nb`: New Brunswick + +- `qc`: Quebec + +- `on`: Ontario + +- `mb`: Manitoba + +- `sk`: Saskatchewan + +- `ab`: Alberta + +- `bc`: British Columbia + +- `yt`: Yukon + +- `nt`: Northwest Territories + +- `nu`: Nunavut + +**`lab`:** The laboratories reporting lab tests. As a note, only Ontario, Quebec and occasionally Saskatchewan have counts from dis-aggregated labs. + +- **NOTE**: Over time, some laboratories were expanded and renamed: + + - CHEO -\> EORLA + + - Sunnybrook Women’s College HSC -\> Shared Hospital Laboratory + + - Toronto Medical Laboratory -\> University Health Network/Mount Sinai Hospital + +**`region`:** The provinces and territories are also sometimes aggregated into six geographic regions: + +- `atlantic`: Newfoundland and Labrador, Prince Edward Island, Nova Scotia and New Brunswick + +- `prairies`: Manitoba, Saskatchewan and Alberta + +- `territories`: Nunavut, Northwest Territories and Yukon + +- `on`: Ontario + +- `qc`: Quebec + +- `bc`: British Columbia + +**Nation:** ISO 3166-1 alpha-2 [country codes](https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2). The only nation we have data on is Canada, abbreviated to `ca` + +**NOTE**: Some of the regions are just stand alone provinces. In this cases: + +- BC, Ontario and Quebec are provinces, but are also their own regions, so data relating to these provinces with `geo_type = region` and `geo_type = province` are the same. + +## Calculation of Percent Positive Lab Tests + +For each respiratory virus, the number of lab tests and number of positive lab tests are reported. For convenience, we calculate the percentage of positive tests for a given virus as: + +$$\text{Percent Positive Lab Tests} = \frac{\text{Number of Positive Tests}}{\text{Number of Tests}} \times 100$$ + +Percent positive lab tests ranges from 0-100%. For HPIV, total HPIV positive tests are not always reported, so we manually calculate them by summing up the positive tests for all HPIV subtypes: + +$$ +\text{HPIV Positive Tests} = \sum\text{HPIV}_\text{subtype} +$$ + +for subtype = 1,2,3,4 and other + +For most of the historic data before the end of the 2023-2024 season, number of positive tests were manually calculated when only percent positive lab tests and number of lab tests were available: + +$$\text{Number Positive Lab Tests} = \frac{\text{Percent Positive Lab Tests}}{100} \times \text{Number of Tests}$$ + +These were not rounded, so there are some decimal values. + +## Data Versioning + +Epiweeks end on Saturday, and the data is usually updated the following Thursday or Friday. While the data was being reported with weekly reports, the version/issue was the date the webpage was modified. If this date was more than 14 days after the epiweek being reported, we set the version to 5 days after the end of epiweek being reported, as this is usually when the data is updated. This should only be a consideration for the historic reports, as the new dashboard states when it was last updated. + +## Limitations + +This data reports the results of laboratory testing of respiratory viruses, which only represents a subset of people who may be sick. People with mild symptoms may be excluded, and there may be a delay between someone developing symptoms and the getting the results of a lab test. + +Data comes from labs across Canada, and some provinces only have one reporting lab, with no further information, so there may be bias if it is easier/faster for people in more densely populated areas to have lab tests done than those in rural locations. + +## Missingness + +There are multiple abbreviations/terms used to denote missing data: + +- N.C : Not collected +- N.R : Data not reported for current week +- N.A : Not available +- Not tested + +For convenience, we treat all these as NA, but there may be subtle differences. + +For epiweeks 5 and 47 of the 2019-2020 season, the reports are empty, so data from these weeks are missing. + +## Lag and Backfill + +Data is reported around \~5 days after the end of an epiweek, up to and including the epiweek, so there is usually a lag of around 5 days. For June-August 2025, the dashboard containing the data was updated biweekly, so there was additional lag. + +The data experiences backfill as counts are finalized in subsequent weeks. + +## Source and Licensing + +This source is derived from the respiratory virus detection data reported by PHAC, originally reported in [weekly reports](https://www.canada.ca/en/public-health/services/surveillance/respiratory-virus-detections-canada.html), and currently reported in a [dynamic dashboard](https://health-infobase.canada.ca/respiratory-virus-surveillance/?source=rvdss). It has been collected and processed for forecasting convenience. + +The data is made available under the [Open Government Licence - Canada](https://open.canada.ca/en/open-government-licence-canada).