From 1598073d432cfb819050c25f73101fad2ce4da9c Mon Sep 17 00:00:00 2001 From: cchuong Date: Fri, 29 Aug 2025 03:23:02 -0700 Subject: [PATCH 1/5] 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 2/5] 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 3/5] 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 4/5] 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 5/5] 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: