From 1598073d432cfb819050c25f73101fad2ce4da9c Mon Sep 17 00:00:00 2001 From: cchuong Date: Fri, 29 Aug 2025 03:23:02 -0700 Subject: [PATCH 1/8] Add documentation for RVDSS endpoint --- docs/api/rvdss.md | 389 ++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 389 insertions(+) create mode 100644 docs/api/rvdss.md diff --git a/docs/api/rvdss.md b/docs/api/rvdss.md new file mode 100644 index 000000000..1699dea2e --- /dev/null +++ b/docs/api/rvdss.md @@ -0,0 +1,389 @@ +--- +title: Respiratory Virus Detections in Canada +parent: Data Sources and Signals +grand_parent: Other Endpoints (COVID-19 and Other Diseases) +nav_order: 1 +editor_options: + markdown: + wrap: 72 +--- + +# Respiratory Virus Detections in Canada + +{: .no_toc} + +- **Source name:** `rvdss` +- **Earliest issue available:** Epiweek 35 2013 (2013-08-31) #change + to first reconstructed issue +- **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 | ++------------------------+--------------------------------------------+ +| `sa | Number of Positive SARS-CoV-2 laboratory | +| rscov2_positive_tests` | tests | +| | | +| | **Earliest Date Available:** 2022-09-03 | ++------------------------+--------------------------------------------+ +| ` | Percentage of SARS-CoV-2 laboratory tests | +| sarscov2_pct_positive` | 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 | ++------------------------+--------------------------------------------+ +| `fluah1n | Number of positive Influenza A(H1N1)pdm09 | +| 1pdm09_positive_tests` | laboratory tests | +| | | +| | **Earliest Date Available:** 2013-08-31 | ++------------------------+--------------------------------------------+ +| ` | Number of positive Influenza A(H1N1)pdm09 | +| fluah3_positive_tests` | laboratory tests | +| | | +| | **Earliest Date Available:** 2013-08-31 | ++------------------------+--------------------------------------------+ +| `f | Number of positive Influenza A(H3N2) | +| luauns_positive_tests` | 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 | ++------------------------+--------------------------------------------+ +| `hpi | Number of positive other HPIV laboratory | +| vother_positive_tests` | 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, some of the +laboratory names are just province/territory names. + +**`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, same as in `lab` and `province` + +- `qc`: Quebec, same as in `lab` and `province` + +- `bc`: British Columbia, same as in `lab` and `province` + +**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 lab names are just the names of individual provinces. +Some of the regions are also just stand alone provinces. In these cases, +the data with `geo_type` = "lab", "province", or "region" are the same, +and are maintained for convenience. + +## 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 + +## 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. + +Standard errors and sample sizes are not available for this data source. + +## 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). From bad8f687d7833c679735af49cde87f9ae8ff63bd Mon Sep 17 00:00:00 2001 From: cchuong <66857147+cchuong@users.noreply.github.com> Date: Fri, 29 Aug 2025 03:42:38 -0700 Subject: [PATCH 2/8] Update rvdss.md Fix markdown formatting --- docs/api/rvdss.md | 248 ++++++++-------------------------------------- 1 file changed, 44 insertions(+), 204 deletions(-) diff --git a/docs/api/rvdss.md b/docs/api/rvdss.md index 1699dea2e..6b3f1a0cc 100644 --- a/docs/api/rvdss.md +++ b/docs/api/rvdss.md @@ -3,9 +3,6 @@ title: Respiratory Virus Detections in Canada parent: Data Sources and Signals grand_parent: Other Endpoints (COVID-19 and Other Diseases) nav_order: 1 -editor_options: - markdown: - wrap: 72 --- # Respiratory Virus Detections in Canada @@ -35,207 +32,50 @@ 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 | -+------------------------+--------------------------------------------+ -| `sa | Number of Positive SARS-CoV-2 laboratory | -| rscov2_positive_tests` | tests | -| | | -| | **Earliest Date Available:** 2022-09-03 | -+------------------------+--------------------------------------------+ -| ` | Percentage of SARS-CoV-2 laboratory tests | -| sarscov2_pct_positive` | 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 | -+------------------------+--------------------------------------------+ -| `fluah1n | Number of positive Influenza A(H1N1)pdm09 | -| 1pdm09_positive_tests` | laboratory tests | -| | | -| | **Earliest Date Available:** 2013-08-31 | -+------------------------+--------------------------------------------+ -| ` | Number of positive Influenza A(H1N1)pdm09 | -| fluah3_positive_tests` | laboratory tests | -| | | -| | **Earliest Date Available:** 2013-08-31 | -+------------------------+--------------------------------------------+ -| `f | Number of positive Influenza A(H3N2) | -| luauns_positive_tests` | 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 | -+------------------------+--------------------------------------------+ -| `hpi | Number of positive other HPIV laboratory | -| vother_positive_tests` | 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 | -+------------------------+--------------------------------------------+ +|---|---| +| `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 @@ -243,7 +83,7 @@ NOTE: Pandemic COVID-19 is not reported in this data source. 1. TOC {:toc} -## Geography {#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 From 6d832b19dfe812e58b7d088090088a6a28c3e4c9 Mon Sep 17 00:00:00 2001 From: cchuong <66857147+cchuong@users.noreply.github.com> Date: Fri, 29 Aug 2025 03:47:35 -0700 Subject: [PATCH 3/8] Change earliest issue to first revision --- docs/api/rvdss.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/api/rvdss.md b/docs/api/rvdss.md index 6b3f1a0cc..870a27114 100644 --- a/docs/api/rvdss.md +++ b/docs/api/rvdss.md @@ -10,8 +10,7 @@ nav_order: 1 {: .no_toc} - **Source name:** `rvdss` -- **Earliest issue available:** Epiweek 35 2013 (2013-08-31) #change - to first reconstructed issue +- **Earliest issue available:** Epiweek 36 2013 (2013-09-07) - **Date of last change:** Never - **Available for:** province, lab, region, nation (see [Geography](#geography)) From f8e31817acbc2fd7028fad4ff849bbfc8ed90a80 Mon Sep 17 00:00:00 2001 From: cchuong Date: Fri, 3 Oct 2025 00:54:54 -0700 Subject: [PATCH 4/8] Update rvdss.md --- docs/api/rvdss.md | 201 ++++++++++++++++++---------------------------- 1 file changed, 77 insertions(+), 124 deletions(-) diff --git a/docs/api/rvdss.md b/docs/api/rvdss.md index 870a27114..3918912c7 100644 --- a/docs/api/rvdss.md +++ b/docs/api/rvdss.md @@ -10,71 +10,60 @@ nav_order: 1 {: .no_toc} - **Source name:** `rvdss` -- **Earliest issue available:** Epiweek 36 2013 (2013-09-07) +- **Earliest issue available:** Epiweek 36 2013 (2013-09-07) - **Date of last change:** Never -- **Available for:** province, lab, region, nation (see - [Geography](#geography)) +- **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. +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| +| 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 @@ -82,15 +71,11 @@ NOTE: Pandemic COVID-19 is not reported in this data source. 1. TOC {:toc} -## Geography +## 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: +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) +**`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 @@ -118,45 +103,35 @@ codes](https://www.canada.ca/en/government/system/digital-government/digital-gov - `nu`: Nunavut -**`lab`:** The laboratories reporting lab tests. As a note, some of the -laboratory names are just province/territory names. +**`lab`:** The laboratories reporting lab tests. As a note, only Ontario, Quebec and occasionaly Saskatchewan have counts from dis-aggregated labs. -**`region`:** The provinces and territories are also sometimes -aggregated into six geographic regions: +**`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 +- `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, same as in `lab` and `province` +- `on`: Ontario + +- `qc`: Quebec -- `qc`: Quebec, same as in `lab` and `province` +- `bc`: British Columbia -- `bc`: British Columbia, same as in `lab` and `province` +**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` -**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: -**NOTE**: Some lab names are just the names of individual provinces. -Some of the regions are also just stand alone provinces. In these cases, -the data with `geo_type` = "lab", "province", or "region" are the same, -and are maintained for convenience. +- 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: +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: +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: $$ \text{HPIV Positive Tests} = \sum\text{HPIV}_\text{subtype} @@ -164,31 +139,21 @@ $$ 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. +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. +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. -Standard errors and sample sizes are not available for this data source. +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 @@ -199,30 +164,18 @@ There are multiple abbreviations/terms used to denote missing data: - N.A : Not available - Not tested -For convenience, we treat all these as NA, but there may be subtle -differences. +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. +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. +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. +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. +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). +The data is made available under the [Open Government Licence - Canada](https://open.canada.ca/en/open-government-licence-canada). From cfebf454f4ff378c4be27552f01ccf9dcda0218d Mon Sep 17 00:00:00 2001 From: cchuong Date: Fri, 3 Oct 2025 01:00:35 -0700 Subject: [PATCH 5/8] Add note on labs that have been renamed/expanded --- docs/api/rvdss.md | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/docs/api/rvdss.md b/docs/api/rvdss.md index 3918912c7..c5a661db0 100644 --- a/docs/api/rvdss.md +++ b/docs/api/rvdss.md @@ -21,7 +21,7 @@ This data source of respiratory virus detections in Canada is collected by the [ 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 | @@ -103,7 +103,15 @@ Unlike most other sources in the Delphi Epidata API, this data source is Canadia - `nu`: Nunavut -**`lab`:** The laboratories reporting lab tests. As a note, only Ontario, Quebec and occasionaly Saskatchewan have counts from dis-aggregated labs. +**`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: From 836ed724c57247ee2741cc53dfff34270a63cb72 Mon Sep 17 00:00:00 2001 From: cchuong Date: Fri, 24 Oct 2025 02:39:48 -0700 Subject: [PATCH 6/8] add more details on backfill behaviour --- docs/api/rvdss.md | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/docs/api/rvdss.md b/docs/api/rvdss.md index c5a661db0..72ceea3cb 100644 --- a/docs/api/rvdss.md +++ b/docs/api/rvdss.md @@ -21,7 +21,7 @@ This data source of respiratory virus detections in Canada is collected by the [ 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 | @@ -180,7 +180,17 @@ For epiweeks 5 and 47 of the 2019-2020 season, the reports are empty, so data fr 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. +The data experiences backfill as counts are finalized in subsequent weeks: + +- Across all indicators, the top 10% observations with the largest relative spread have had values revised by 25-33% or more. + +- `flu_pct_positive`, `flua_pct_positive`, `fluah1n1pdm09_positive_tests` and related indicators have larger spread between updates (\~70-90% of obs have more than 10% relative spread vs 20-30% in other signals). + +- `hpiv1_`,`hpiv2_`,`hpiv3_` and `hpiv4_` indicators rarely have revisions, and across all indicators, most observations have less than 3 revisions (99% of observations). + +- Across all indicators, 90% of observations with revisions are revised to within 20% of their final value (and stay within that 20% range) 1-3 weeks after the time_value the obs is being reported for. + +- 95% of observations with revisions are finalized within 3-4 weeks of the time_value.`sarscov2_*` and `flub_*` indicators are finalized fairly fast (95% finalized after 12 days). `fluah3_positive_tests` and `adv_*` indicators are finalized fairly slowly (95% finalized after 30-40 days). ## Source and Licensing From 201c36b16b15fc27e534985d65b9330c01a78a4a Mon Sep 17 00:00:00 2001 From: cchuong Date: Fri, 7 Nov 2025 12:25:13 -0800 Subject: [PATCH 7/8] remove unused columns --- docs/api/rvdss.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/docs/api/rvdss.md b/docs/api/rvdss.md index 72ceea3cb..ed057ea83 100644 --- a/docs/api/rvdss.md +++ b/docs/api/rvdss.md @@ -21,7 +21,7 @@ This data source of respiratory virus detections in Canada is collected by the [ 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 | @@ -60,10 +60,7 @@ NOTE: Pandemic COVID-19 is not reported in this data source. | `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 From bd110b8c78bb8a97485c12e442d0e3f36f2f4384 Mon Sep 17 00:00:00 2001 From: nmdefries <42820733+nmdefries@users.noreply.github.com> Date: Fri, 7 Nov 2025 19:26:53 -0500 Subject: [PATCH 8/8] clarify indicator meanings, formatting, backfill info --- docs/api/rvdss.md | 181 ++++++++++++++++++++++------------------------ 1 file changed, 85 insertions(+), 96 deletions(-) diff --git a/docs/api/rvdss.md b/docs/api/rvdss.md index ed057ea83..2217e9608 100644 --- a/docs/api/rvdss.md +++ b/docs/api/rvdss.md @@ -9,55 +9,55 @@ nav_order: 1 {: .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** +- **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](#source-and-licensing) -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. +This data source of respiratory virus detections in Canada is collected by the [Respiratory Virus Detection Surveillance System (RVDSS)](https://health-infobase.canada.ca/respiratory-virus-surveillance/about.html) and published by the Public Health Agency of Canada (PHAC). Laboratory tests for various respiratory illnesses are reported on a weekly basis by sentinel laboratories across Canada 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), a subsidiary of PHAC. The data was originally reported in weekly online reports, but since June 2024, has changed to being reported through 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_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 | +| `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 laboratory tests positive for RSV
**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_tests` | Number of human parainfluenza virus (HPIV) laboratory tests (for all subtypes)
**Earliest Date Available:** 2013-08-31 | +| `hpiv1_positive_tests` | Number of HPIV laboratory tests positive for HPIV-1
**Earliest Date Available:** 2013-08-31 | +| `hpiv2_positive_tests` | Number of HPIV laboratory tests positive for HPIV-2
**Earliest Date Available:** 2013-08-31 | +| `hpiv3_positive_tests` | Number of HPIV laboratory tests positive for HPIV-3
**Earliest Date Available:** 2013-08-31 | +| `hpiv4_positive_tests` | Number of HPIV laboratory tests positive for HPIV-4
**Earliest Date Available:** 2013-08-31 | +| `hpivother_positive_tests` | Number of HPIV laboratory tests positive for any other HPIV subtype
**Earliest Date Available:** 2013-08-31 | +| `hpiv_positive_tests` | Number of laboratory tests positive for any HPIV subtype
**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_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_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_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_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 | | `year` | Current year
**Earliest Date Available:** 2023-09-02 | @@ -70,65 +70,52 @@ NOTE: Pandemic COVID-19 is not reported in this data source. ## 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: +Unlike most other sources in the Delphi Epidata API, this data source reports data for Canada. This source is available for sevearl geographic types. Specific regions can be requested using the `geo_value` parameter, as follows. -**`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) +### Geo type `province` -- `nl`: Newfoundland and Labrador +One of the 10 provinces or three territories, abbreviated using [standard 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) -- `pe`: Prince Edward Island +- `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 -- `ns`: Nova Scotia +### Geo type `lab` -- `nb`: New Brunswick +The laboratories reporting lab tests. Only Ontario, Quebec, and occasionally Saskatchewan report counts for individual lab facilities. -- `qc`: Quebec +**NOTE**: Over time, some laboratories were expanded and renamed: -- `on`: Ontario +- Children's Hospital of Eastern Ontario (CHEO) -\> Eastern Ontario Regional Laboratory Association (EORLA) +- Sunnybrook Women’s College Health Sciences Centre -\> Shared Hospital Laboratory +- Toronto Medical Laboratory -\> University Health Network/Mount Sinai Hospital -- `mb`: Manitoba +### Geo type `region` -- `sk`: Saskatchewan +The provinces and territories are also aggregated into six geographic regions: -- `ab`: Alberta +- `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 -- `bc`: British Columbia +### Geo type `nation` -- `yt`: Yukon +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` -- `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. +**NOTE**: Ontario, Quebec, and British Columbia are single-province regions, so data for these provinces is the same using either `geo_type = region` or `geo_type = province`. ## Calculation of Percent Positive Lab Tests @@ -144,11 +131,11 @@ $$ for subtype = 1,2,3,4 and other -For most of the historic data before the end of the 2023-2024 season, number of positive tests were manually calculated when only percent positive lab tests and number of lab tests were available: +Prior to the end of the 2023-2024 season, total tests and percent positivity were reported, but number of positive tests was not explicitly reported. For convenience, we manually calculated number of positive tests when only percent positive lab tests and number of lab tests were available. $$\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. +These values are not rounded, so some are not integers. ## Data Versioning @@ -158,16 +145,16 @@ Epiweeks end on Saturday, and the data is usually updated the following Thursday 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. +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 or 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: +The source uses multiple terms used to denote missing data: -- N.C : Not collected -- N.R : Data not reported for current week -- N.A : Not available -- Not tested +- NC : Not collected +- NR : Data not reported for current week +- NA : Not available +- Not tested For convenience, we treat all these as NA, but there may be subtle differences. @@ -175,22 +162,24 @@ For epiweeks 5 and 47 of the 2019-2020 season, the reports are empty, so data fr ## 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: +Data is reported around \~5 days after the end of an epiweek. For June-August 2025, the dashboard containing the data was updated every two weeks, so the lag during that period was larger. -- Across all indicators, the top 10% observations with the largest relative spread have had values revised by 25-33% or more. +The data experiences backfill as counts are finalized in subsequent weeks. The amount and impact of revisions depend on the virus. -- `flu_pct_positive`, `flua_pct_positive`, `fluah1n1pdm09_positive_tests` and related indicators have larger spread between updates (\~70-90% of obs have more than 10% relative spread vs 20-30% in other signals). +Across all indicators, most (99%) observations have less than 3 revisions. +`hpiv1_*`,`hpiv2_*`,`hpiv3_*` and `hpiv4_*` indicators have revisions even more rarely. -- `hpiv1_`,`hpiv2_`,`hpiv3_` and `hpiv4_` indicators rarely have revisions, and across all indicators, most observations have less than 3 revisions (99% of observations). +Across all indicators, the top 10% of observations (unique location-date pairs) with the largest relative spread have had values revised by 25-33% or more. +However, 90% of observations with revisions are revised to within 20% of their final value (and stay within that 20% range) 1-3 weeks after the date an observation is being reported for. +And 95% of observations with revisions are finalized within 3-4 weeks. +So revisions that greatly impact a reported value happen soon after an observation is first reported. -- Across all indicators, 90% of observations with revisions are revised to within 20% of their final value (and stay within that 20% range) 1-3 weeks after the time_value the obs is being reported for. +Looking at the revision speed of specific indicators, `sarscov2_*` and `flub_*` indicators are finalized fairly fast (95% finalized after 12 days). `fluah3_positive_tests` and `adv_*` indicators are finalized fairly slowly (95% finalized after 30-40 days). -- 95% of observations with revisions are finalized within 3-4 weeks of the time_value.`sarscov2_*` and `flub_*` indicators are finalized fairly fast (95% finalized after 12 days). `fluah3_positive_tests` and `adv_*` indicators are finalized fairly slowly (95% finalized after 30-40 days). +`flu_pct_positive`, `flua_pct_positive`, `fluah1n1pdm09_positive_tests` and related indicators have larger spread than other indicators. That is, \~70-90% of observations have more than 10% relative spread vs 20-30% in other indicators. ## 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. +This source is derived from PHAC's Respiratory Virus Detection Data, 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). The data is made available under the [Open Government Licence - Canada](https://open.canada.ca/en/open-government-licence-canada).