Add RVDSS documentation #1667
There are no files selected for viewing
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,185 @@ | ||
| --- | ||
| title: Respiratory Virus Detections in Canada | ||
| parent: Data Sources and Signals | ||
| grand_parent: Other Endpoints (COVID-19 and Other Diseases) | ||
| nav_order: 1 | ||
| --- | ||
|
|
||
| # Respiratory Virus Detections in Canada | ||
|
|
||
| {: .no_toc} | ||
|
|
||
| - **Source name:** `rvdss` | ||
| - **Earliest issue available:** Epiweek 36 2013 (2013-09-07) | ||
| - **Date of last change:** Never | ||
| - **Available for:** province, lab, region, nation (see [Geography](#geography)) | ||
| - **Time type:** week (see [date format docs](../covidcast_times.md)) | ||
| - **License:** [Open Government Licence - Canada](#source-and-licensing) | ||
|
|
||
| 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 | | ||
|
Contributor
There was a problem hiding this comment. suggestion: we should add the descriptive columns (time_value, issue, etc) to this table so that we can define them and explain the general time formats. |
||
| |--------------------------------|---------------------------------------------------------------------------------------------------------------------------------------------| | ||
| | `sarscov2_tests` | Number of SARS-CoV-2 laboratory tests <br/> **Earliest Date Available:** 2022-09-03 | | ||
|
Contributor
There was a problem hiding this comment. suggestion: Recommend clarifying in the description that SARS-CoV-2 is the virus that causes COVID-19, both for better searching and because people mostly use the name "COVID-19". I guess maybe it's not technically correct to say that this is a "COVID-19 laboratory test" (?), but we could say that too. Second, do we know what kind of tests these are? E.g. antigen, nose swab, NAAT (nucleic acid amplification) |
||
| | `sarscov2_positive_tests` | Number of positive SARS-CoV-2 laboratory tests <br/> **Earliest Date Available:** 2022-09-03 | | ||
| | `sarscov2_pct_positive` | Percentage of SARS-CoV-2 laboratory tests that are positive <br/> **Earliest Date Available:** 2022-09-03 | | ||
| | `flu_tests` | Number of influenza laboratory tests (for all subtypes) <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `flua_tests` | Number of influenza A laboratory tests (Same as `flu_tests`, just maintained for convenience) <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `flub_tests` | Number of influenza B laboratory tests (Same as `flu_tests`, just maintained for convenience) <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `flu_positive_tests` | Number of positive influenza laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `flu_pct_positive` | Percentage of influenza laboratory tests that are positive (for all subtypes) <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `fluah1n1pdm09_positive_tests` | Number of positive influenza A(H1N1)pdm09 laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `fluah3_positive_tests` | Number of positive influenza A(H3N2) laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `fluauns_positive_tests` | Number of positive influenza A (unsubtyped) laboratory tests <br/> **Earliest Date Available:** 2016-09-03 | | ||
| | `flua_positive_tests` | Number of positive influenza A laboratory tests (for all subtypes) <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `flua_pct_positive` | Percentage of influenza A laboratory tests that are positive (for all subtypes) <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `flub_positive_tests` | Number of positive influenza B laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `flub_pct_positive` | Percentage of influenza B laboratory tests that are positive <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `rsv_tests` | Number of respiratory syncytial virus (RSV) laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `rsv_positive_tests` | Number of laboratory tests positive for RSV <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `rsv_pct_positive` | Percentage of RSV laboratory tests that are positive <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hpiv_tests` | Number of human parainfluenza virus (HPIV) laboratory tests (for all subtypes)<br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hpiv1_positive_tests` | Number of HPIV laboratory tests positive for HPIV-1 <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hpiv2_positive_tests` | Number of HPIV laboratory tests positive for HPIV-2 <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hpiv3_positive_tests` | Number of HPIV laboratory tests positive for HPIV-3 <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hpiv4_positive_tests` | Number of HPIV laboratory tests positive for HPIV-4 <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hpivother_positive_tests` | Number of HPIV laboratory tests positive for any other HPIV subtype <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hpiv_positive_tests` | Number of laboratory tests positive for any HPIV subtype <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hpiv_pct_positive` | Percentage of HPIV laboratory tests that are positive (for all subtypes) <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `adv_tests` | Number of adenovirus (ADV) laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `adv_positive_tests` | Number of positive ADV laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `adv_pct_positive` | Percentage of ADV laboratory tests that are positive <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hmpv_tests` | Number of human metapneumovirus (hMPV)laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hmpv_positive_tests` | Number of positive hMPV laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hmpv_pct_positive` | Percentage of hMPV laboratory tests that are positive <br/>**Earliest Date Available:** 2013-08-31 | | ||
| | `evrv_tests` | Number of enterovirus/rhinovirus (EV/RV) laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `evrv_positive_tests` | Number of positive EV/RV laboratory tests <br/>**Earliest Date Available:** 2013-08-31 | | ||
| | `evrv_pct_positive` | Percentage of EV/RV laboratory tests that are positive <br/>**Earliest Date Available:** 2013-08-31 | | ||
| | `hcov_tests` | Number of human coronavirus (HCoV) laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hcov_positive_tests` | Number of positive HCoV laboratory tests <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `hcov_pct_positive` | Percentage of HCoV laboratory tests that are positive <br/> **Earliest Date Available:** 2013-08-31 | | ||
| | `year` | Current year <br/> **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 reports data for Canada. This source is available for sevearl geographic types. Specific regions can be requested using the `geo_value` parameter, as follows. | ||
|
|
||
| ### Geo type `province` | ||
|
|
||
| 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) | ||
|
|
||
| - `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 | ||
|
|
||
| ### Geo type `lab` | ||
|
|
||
| The laboratories reporting lab tests. Only Ontario, Quebec, and occasionally Saskatchewan report counts for individual lab facilities. | ||
|
|
||
| **NOTE**: Over time, some laboratories were expanded and renamed: | ||
|
|
||
| - 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 | ||
|
|
||
| ### Geo type `region` | ||
|
|
||
| The provinces and territories are also 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 | ||
|
|
||
| ### Geo type `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**: 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 | ||
|
|
||
| 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 | ||
|
|
||
| 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 values are not rounded, so some are not integers. | ||
|
|
||
| ## 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 or faster for people in more densely populated areas to have lab tests done than those in rural locations. | ||
|
|
||
| ## Missingness | ||
|
|
||
| The source uses multiple terms used to denote missing data: | ||
|
|
||
| - 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. | ||
|
|
||
| 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. For June-August 2025, the dashboard containing the data was updated every two weeks, so the lag during that period was larger. | ||
|
|
||
| The data experiences backfill as counts are finalized in subsequent weeks. The amount and impact of revisions depend on the virus. | ||
|
|
||
| Across all indicators, most (99%) observations have less than 3 revisions. | ||
| `hpiv1_*`,`hpiv2_*`,`hpiv3_*` and `hpiv4_*` indicators have revisions even more rarely. | ||
|
|
||
| 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. | ||
|
|
||
| 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). | ||
|
|
||
| `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 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). | ||
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
question: Not sure what you mean here. Doesn't this source report COVID data for the COVID pandemic time period?