extra_data

Extra datasets

This repository contains several datasets that do not fit into the main datasets. They are located in the extra_data directory and described below.

Wastewater data

• Public Health Agency of Canada wastewater dataset (extra_data/phac_wastewater/phac_wastewater.csv)
  • The Public Health Agency of Canada (PHAC) maintains a wastewater surveillance dataset with time series of SARS-CoV-2 viral load (copies/mL) for participating wastewater surveillance sites from across the country. This dataset has been reproduced here in a convenient format. All sites have a value for region (province/territory) and sub_region_1 (city or region). Some sites also have multiple values for sub_region_2 (neighbourhood or specific facility within a city), such as Toronto having Ashbridges Bay, Highland Creek, Humber, and North Toronto. See the Public Health Agency of Canada's technical notes for aid with interpretation of the data.

Excess mortality data

• Statistics Canada excess mortality dataset (extra_data/statcan_excess_mortality/statcan_excess_mortality.csv)
  • Statistics Canada maintains an excess mortality dataset (Table 13-10-0784-01) which contains estimates of expected deaths and excess deaths for Canada and each province and territory, beginning with the week ending 2020-01-04. This dataset has been reproduced here in a convenient format. The file release_date.txt gives the release date of the latest Statistics Canada dataset.

Extra case data

• A time series of individual-level data for all confirmed cases of COVID-19 reported to the Public Health Agency of Canada (extra_data/phac_individual_ts/phac_individual_ts.csv)
  • The Public Health Agency of Canada (PHAC) maintains an individual-level case dataset entitled Preliminary dataset on confirmed cases of COVID-19, Public Health Agency of Canada. This dataset transform the PHAC dataset into a weekly time series with case counts by region, gender, and age group. It also gives hospital status and death status for each case, if known. The user guide and data dictionary explains the meaning of each variable and further describes the details and limitations of the dataset. The file release_date.txt gives the release date of the latest PHAC dataset.
• Case and testing data for the Territories from the Respiratory Virus Detection Surveillance System (RVDSS) since the week of 2022-09-03 (extra_data/territories_rvdss_since_2022-09-03/territories_rvdss_since_2022-09-03.csv)
  • The Territories have stopped reporting case (NT: 2022-06-13; NU: 2022-04-05; YT: 2022-11-10) and testing (NT: 2022-11-17; NU: 2022-11-20; YT: 2022-11-10) data for COVID-19. However, the Respiratory Virus Detection Surveillance System (RVDSS) has reported COVID-19 testing and test positivity data for all provinces and territories since the week ending 2022-09-03. Weekly case counts can be calculated from these two values. These data have not been incorporated into the main dataset for a variety of reasons. In the case of NT and NU, there is a gap of several months between when these territories stopped reporting cases and when the RVDSS dataset become available. There are also several weeks of missing data for NT in the RVDSS dataset. In the case of YT, the testing numbers reported in the RVDSS dataset are much higher than the testing numbers reporting in the YT dashboard dataset or the previous PHAC dataset (SALT) for the period that these datasets overlap, raising questions about the compatibility of the data. There are also discrepencies in the the derived case counts from RVDSS compared to the case counts reported on the YT dashboard during the overlapping period. With these caveats in mind, case, testing, and percent positivity values for the Territories since the week ending 2022-09-03 are reported in this extra dataset.

Extra hospital/ICU data

• Extra hospital/ICU occupancy or admission data (extra_data/hospital_icu_extra/hosp_icu_extra.csv)
  • This dataset contains extra hospital/ICU occupancy and admission data that are not included in the main hospital/ICU occupancy and admission datasets. This mainly consists of data distinguishing hospital occupancy or admissions "for" or "with" COVID-19, whenever such distinctions were made in the source dataset. The exact meaning of each column is described in the README file.
• Canadian Critical Care Society (CCCS) hospitalization/ICU time series (extra_data/cccs_hospitalization_icu/cccs_hospitalization_icu_ts.csv)
  • This dataset converts the CCCS hospitalization/ICU dataset into a time series. Originally, the dataset sought to capture hospital/ICU occupancy numbers (noting that total hospitalization numbers include total ICU numbers), but began to include different numbers (such as hosital/ICU admissions) as data availability changed. For this reason, the dataset should not be relied upon with reading the notes associated with each update. These notes are available as cccs_hospitalization_icu_ts_notes.json and provide important context (such as definitions) for the numbers included in each data update.

Province-specific extra data

• Biweekly, incomplete health region-level case data for Saskatchewan (extra_data/sk_biweekly_cases_hr/sk_biweekly_cases_hr.csv)
  • Beginning with the CRISP report covering the week of 2022-12-25–2022-12-31, Saskathewan began reporting health-region level case data after a long period of reporting cases only at the province level. However, the health region-level data are 1) incomplete (many values are listed as having unknown/out of province health region, but they are never updated in future reports) and 2) only cover the second of the two weeks of data presented in each report (the first week is reported at the province level only). For these two reasons, plus the fact that the province only reported province-level case data for some time before this, we opted not to include these data in the main SK case time series, instead sticking with reporting province-level case data. However, these data are reported here in this extra dataset.
• Extra Respiratory Watch data for Nova Scotia (extra_data/ns_extra_respiratory_watch/ns_extra_respiratory_watch.csv)
  • Nova Scotia's Respiratory Watch report, introduced for the reporting period beginning 2023-08-27, gives some data not included in the main dataset. This includes health region-level case data, which had not been reported by the province for a long time, as well as ICU admission data, which had not been previously reported by the province (despite reporting hospital admission data for some time). These data are reported here in this extra dataset.
  • The following note applies to the hospital/ICU admission data: "Hospital and ICU admissions are undercounted in the source dataset for the following reason: 'In this table, only the most severe outcome for a case is included; numbers of hospitalizations and ICU admissions could therefore decline over time, if a person counted in one of those columns moves to a more severe outcome.' Note that we calculated hospital admissions as the sum of non-ICU and ICU hospital admissions, so a patient moving from the non-ICU to the ICU category would not affect the accuracy of this value, only deaths would."