2022-11-14 / Goodbye

This repository is now being archived (set to read-only).

We, the Sykdomspulsen team, hope that the easy accessibility of machine-readable data helped you, the user, in whatever task you were doing.

Feel free to contact us at [email protected]

Sykdomspulsen team

2022-11-14 / Last date of data delivery

Please note that today is the last day that data will be delivered to this repository.

2022-11-11 / Shutting down the repository (Norsk)

Kjære bruker av Sykdomspulsens leveranser

Vi viser til tidligere kommunikasjon fra Folkehelseinstituttet med varsel om sannsynlig nedstengning av GitHub til media i høst. Vi har jobbet intenst de siste ukene med å finne alternative løsninger, men ser oss dessverre nødt til å stenge ned nettsiden fra 15. november. Vi har forståelse for at bortfall av disse leveransene vil medføre ulemper for dere brukere, men i den krevende budsjettsituasjonen vi står i blir vi dessverre nødt til å gjøre strenge prioriteringer, selv om vi vet det får konsekvenser for dere som mottar denne typen tjenester. Vi vil i tiden fremover jobbe videre for å finne løsninger på sikt, og ber om forståelse for at dette kan ta noe tid.

Statistikk på nasjonalt og regionalt nivå både på covid-19-smitte og vaksinasjon finnes på https://statistikk.fhi.no, og ukentlige nøkkeltall vil bli levert i ukerapporten for covid-19, influensa og andre luftveisinfeksjoner.

Vennlig hilsen

Trygve Ottersen

Områdedirektør Smittevern FHI

2022-11-11 / Shutting down the repository (English)

Dear users of our GitHub repository (https://github.com/folkehelseinstituttet/surveillance_data/),

With reference to the note on the 2022-10-14, FHI/NIPH has worked intensively the past few weeks to find alternative solutions, but unfortunately do not see any other solution besides shutting the repository down on 2022-11-15. FHI/NIPH understands that the removal of this repository will have negative consequences for the users, but in this difficult budget situation FHI/NIPH must make such decisions, even though FHI/NIPH knows that this has consequences for the users of this service. FHI/NIPH will work in the future to find solutions, and FHI/NIPH asks the users to understand that this can take time.

Statistics on the national and regional level (both for covid-19 infectious and vaccinations) can be found at https://statistikk.fhi.no, and weekly key indicators will be delivered in the weekly report for covid-19, influenza, and other respiratory infections.

Kind regards

Trygve Ottersen

Area Director for Infectious Diseases

Folkehelseinstituttet

2022-10-14 / Shutting down the repository

Dear users of our GitHub repository (https://github.com/folkehelseinstituttet/surveillance_data/),

With reference to the note on the 2022-09-19, FHI/NIPH understands that the that a possible loss of these deliveries will cause major inconvenience for the users, but in the demanding budget situation FHI/NIPH is in, FHI/NIPH will unfortunately have to make strict prioritizations that have consequences for recipients of FHI/NIPH services.

FHI/NIPH has now decided to postpone the shutdown for a few weeks while FHI/NIPH works to find alternative solutions. Unfortunately, you users must be prepared that there may be a period where some of FHI/NIPH services are not available, and some may eventually completely disappear.

FHI/NIPH will keep its users informed about the situation.

If you have any questions or feedback, please send an e-mail to Sykdomspulsen ([email protected]).

All the best,

Sykdomspulsen team

2022-09-19 / Shutting down the repository

Dear users of our GitHub repository (https://github.com/folkehelseinstituttet/surveillance_data/),

FHI/NIPH is in the middle of a budget process, which entails that we have to look into areas where we can reduce our costs. One of the measures in this process will, amongst others, include workforce reductions and a prioritization of the products/deliveries we can continue to deliver. Sykdomspulsen's team and its deliveries are unfortunately no exception. Sykdomspulsen's team will most likely have to reduce its workforce substantially. This entails that we probably will not be able to continue to deliver data to this GitHub repository.

At this point we find it necessary to give you the unfortunate news that our deliverable "Surveillance data on GitHub" (https://github.com/folkehelseinstituttet/surveillance_data) will most likely stop from the 14th of October 2022.

We are sorry for the inconvenience this might be for you. We hope that this message will give you the opportunity to find another alternative.

If you have any questions or feedback, please send an e-mail to Sykdomspulsen ([email protected]).

All the best,

Sykdomspulsen team

Available COVID-19 datasets

• covid19/data_covid19_demographics_YYYY_MM_DD First published 2020-06-25. Contains demographic information about deaths.
• covid19/data_covid19_hospital_by_time_YYYY_MM_DD First published 2020-06-23. Contains information about number of people in hospitals and ICUs with COVID-19 as the primary cause.
• covid19/data_covid19_lab_by_time_YYYY_MM_DD First published 2020-06-23. Contains information about the number of people tested for COVID-19.
• covid19/data_covid19_msis_by_location_YYYY_MM_DD First published 2020-06-04. Contains the number of people diagnosed with COVID-19 per location.
• covid19/data_covid19_msis_by_time_location_YYYY_MM_DD First published 2020-04-24. Contains the number of people diagnosed with COVID-19 per location and day (i.e. epicurves).
• covid19/data_covid19_msis_by_time_sex_age_YYYY_MM_DD First published 2020-06-23. Contains information about the sex/age of people diagnosed with COVID-19 over time.
• covid19/data_covid19_sysvak_by_location_YYYY_MM_DD First published 2021-01-20. Contains the number of people who have been vaccinated for COVID-19 per location.
• covid19/data_covid19_sysvak_by_time_location_YYYY_MM_DD First published 2021-01-20. Contains the number of people who have been vaccinated for COVID-19 per location and day.

Important notes

• 2022-11-02: Due to technical problems in Beredt C-19, data on hospitalisations and ICUs from NoPaR and NIR have not been updated today. Beredt C-19 is working to rectify the problem.

• 2022-08-25: Due to technical problems in NoPaR/NIR, data on hospitalisations and ICUs have not been updated today. NoPaR/NIR is working to rectify the problem.

• 2022-06-20: The 4th.dose of the covid-19 vaccine has been added to our statistics. The age groups have been changed from 75-84 years to 75-79 years and 80-84 years. This change in age groups will apply to all our data for covid-19 vaccination (including historical data). For dose 1, 2 and 3 the data will be censored if the 75-79 or 80-84 age group has fewer than 5 cases before 20th of June 2022. This is because data for the entire age group 75-84 have been available and when comparing old and new age groups can show less than 5. N.B. Sex and age groups will not be available on municipal level due to censoring.

• 2022-06-08: Due to technical problems in SYSVAK, data on vaccination have not been updated today. SYSVAK is working to rectify the problem.

• 2022-04-04: Data for hospitalization all causes will no longer be presented as a part of the covid-19 statistics. This is due to the fact that it no longer gets updated from NoPAR and will give an underestimated number.

• 2022-03-18: Due to technical problems in SYSVAK, data on covid-19 vaccination have not been updated since 16th of March. SYSVAK is working to rectify the problem.

• 2022-03.17: The Covid-19 deaths data will from this date come from DÅR via Beredt C-19 instead of from MSIS. This is because the DÅR data is more up to date at this point. The new file will get a new name and the file will not include sex, age and counties. The file will be updated every Tuesday morning.

• 2022-03-14: Due to technical problems in SYSVAK, data on covid-19 vaccination have not been updated since 10th of March. SYSVAK is working to rectify the problem.

• 2022-03-07: Norwegian population data from 2022 is going to be used starting from 2022-03-10. Relevant changes are made in the R package fhidata. Affected datasets are norway_population_by_age_b2020, norway_population_by_age_sex_b2020; affected functions are norway_population_by_age_b2020, norway_population_by_age_sex_b2020.

• 2022-02-03: There has been changes in the data from SYSVAK for covid-19 vaccination, which means that individuals with old municipality or county number will be registered as “unknown”. The change also applies to data back in time.

• 2022-01-27: The calculation of age for vaccinated individuals has changed from age at time of vaccination to age calculated as year of vaccination minus birth year. This means age will be presented as age groups(cohorts) after year of vaccination. The change also applies to data back in time.

• 2022-01-24: Persons with a 3rd dose (refreshment dose) or 2 doses of corona vaccination and have undergone covid-19 the last 3 months will as a general rule no longer be offered a confirmatory PCR test. This will affect the number of cases reported to MSIS, primarily in the population over the age of 18, where we will capture a lower proportion of those infected than before. Data on reported cases are therefore not directly comparable over time.

• 2022-01-21: The number of Covid-19 cases from Furst laboratories has been delayed in MSIS. This will be updated in the next few days. Once updated, the result will be that the number of cases registered from 15. January will increase by approx 5000-8000.

• 2022-01-05: The vaccination data may be different in this site compared to the covid-19 weekly report. This is because the denominator used in this site is based on SSB-data while the weekly report is based on Folkeregister-data. In addition, in the weekly report the age is calculated as of 31-12-2022 (whole yearly cohorts), while this page gives vaccination data based on age at date of vaccination.

• 2021-11-18: The SYSVAK data published today (2021-11-18) at the municipality level was incorrect. The error has been corrected in the data published 2021-11-19.

• 2021-10-26: NIPaR data (hospitalisations) has not been updated because of problems with the NIPaR database. It is expected to be updated tomorrow (27th of October).

• 2021-09-08: SYSVAK data has not been updated today because of problems with the SYSVAK database

• 2021-06-30: The number of tested in this github data is not identical to the number of tested in the weekly covid-19 report made by FHI today. This is because the weekly report do include PCR and Antigen test, while this data only include only PCR tested.

• 2021-06-11: SYSVAK data has not been updated today because of problems with the SYSVAK database

• 2021-06-07: SYSVAK data has not been updated today because of problems with the SYSVAK database.

• 2021-04-30: There was earlier some missing values in the covid-19 SYSVAK data, this has been fixed, but can cause changes in the numbers in some areas.

• 2021-04-16: There is an error in the file from 2021_04_16, PLEASE DO NOT USE THIS FILE.

• From 2021_04_19: There is a change in the dates displayed in the file "data_covid19_lab_by_time_". This file will from this point only show data from 2020_04_01. This is because of a change to using MSIS data instead of laboratory data.

Note about "missing data" in the covid19 folder

Because we have uploaded over 1000 data files to the covid19 folder, some files are no longer directly viewable from the browser.

There are three ways that you can obtain your data:

1. Download the entire data repository https://github.com/folkehelseinstituttet/surveillance_data/archive/master.zip
2. Use a desktop program (e.g. https://desktop.github.com/) to syncronize the repository to your computer (this is similar to a manual dropbox/onedrive/google drive sync). The following links can be useful:
   • https://docs.github.com/en/free-pro-team@latest/desktop/contributing-and-collaborating-using-github-desktop/cloning-a-repository-from-github-to-github-desktop
   • https://docs.github.com/en/free-pro-team@latest/desktop/contributing-and-collaborating-using-github-desktop/syncing-your-branch#pulling-to-your-local-branch-from-the-remote
3. Directly "knowing" the link of the data file you are interested in (e.g. https://github.com/folkehelseinstituttet/surveillance_data/blob/master/covid19/data_covid19_msis_by_time_location_2020-11-23.csv)

We recommend that you use either solution #1 or #2.

surveillance_data

This is a frequently updated repository for Norwegian surveillance data from Folkehelseinstituttet (Norwegian Institute of Public Health).

The purpose of this repository is to make surveillance data easily accessible from a machine-reading perspective.

Documentation for each dataset is available in text files beginning with _DOCUMENTATION_

If something does not appear to be correct, or more documentation is needed in a particular area, or you have suggestions about the way the data is presented/formatted, please email the following three email addresses simultaneously: [email protected], [email protected], and [email protected]