Merge pull request #1159 from ScilifelabDataCentre/Hamsa/Freya-179

Hamsa/freya 179

content/english/dashboards/vaccines.md

@@ -49,9 +49,9 @@ For more information on vaccination in Sweden, please also see the [RECOVAC dash
 
 <div class="alert alert-info">The visualisations on this page were last updated: <span id="visualisations_date_modified">2023-03-24</span>.</div>
 
-The [Swedish Health Agency (Folkhälsomyndigheten, FoHM)](https://folkhalsomyndigheten.se) provide information, summary statistics, and data related to COVID-19 vaccination in Sweden [(only available in Swedish)](https://www.folkhalsomyndigheten.se/folkhalsorapportering-statistik/statistikdatabaser-och-visualisering/vaccinationsstatistik/statistik-for-vaccination-mot-covid-19/). The visualisations below are based on the publicly available COVID-19 vaccination data from FoHM, which can be [downloaded directly](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data). For each visualisation, we describe which data in the dataset were used, how calculations were completed, and provide a link to the script(s) used to produce it.
+The [Swedish Health Agency (Folkhälsomyndigheten, FoHM)](https://folkhalsomyndigheten.se) provide information, summary statistics, and data related to COVID-19 vaccination in Sweden [(only available in Swedish)](https://www.folkhalsomyndigheten.se/folkhalsorapportering-statistik/statistikdatabaser-och-visualisering/vaccinationsstatistik/statistik-for-vaccination-mot-covid-19/). The visualisations below are based on the publicly available COVID-19 vaccination data from FoHM, which can be [downloaded directly](https://blobserver.dc.scilifelab.se/blob/Folkhalsomyndigheten_Covid19_Vaccine-93.xlsx). For each visualisation, we describe which data in the dataset were used, how calculations were completed, and provide a link to the script(s) used to produce it.
 
-The source data is updated weekly (on Thursdays), and the visualisations on this page will be updated shortly thereafter (usually on Fridays). All of our code related to this page is available on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Vaccine_page). All of the vaccine data is processed using a single [data preparation script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_dataprep_Swedentots.py). The code required to generate each visualisation/number set is linked close to the corresponding plot/text.
+ All of our code related to this page is available on [GitHub](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/tree/main/Vaccine_page). All of the vaccine data is processed using a single [data preparation script](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/Vaccine_page/vaccine_dataprep_Swedentots.py). The code required to generate each visualisation/number set is linked close to the corresponding plot/text.
 
 ### General summary statistics
 
@@ -65,7 +65,7 @@ In the chart below, we show vaccine coverage as calculated using the 'whole popu
 
 Please note, we refer to the number of doses administered (at least) for simplicity. However, other sources may use specific names/classifications to refer to different doses. For example, individuals given at least 2 doses may be considered 'fully vaccinated'. The third dose is also sometimes referred to as a 'booster dose'. Individuals with at least 3 doses are thus sometimes said to be 'fully vaccinated with a booster dose'. Other variations also exist, and other terms may arise as subsequent doses becomes more widely available.
 
-Vaccination data is spread between multiple tabs of the [FoHM data file](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data). For calculations done using the 'eligible population method', we used percentage data from the 'Vaccinerade tidsserie', 'Vaccinerade tidsserie dos 3', 'Vaccinerade tidsserie dos 4', and 'Vaccinerade tidsserie dos 5' tabs of the [FoHM data file](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data). These tabs contained data about the amount of individuals that received at least one or two doses, at least 3 doses, at least 4 doses, and at least 5 doses, respectively. For the 'whole population method', we use the latest population data from [Statistics Sweden (SCB)](https://www.scb.se/) and the most recent 'raw number' of the doses administered from same tabs in the [FoHM data file](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data).
+Vaccination data is spread between multiple tabs of the [FoHM data file](https://blobserver.dc.scilifelab.se/blob/Folkhalsomyndigheten_Covid19_Vaccine-93.xlsx). For calculations done using the 'eligible population method', we used percentage data from the 'Vaccinerade tidsserie', 'Vaccinerade tidsserie dos 3', 'Vaccinerade tidsserie dos 4', and 'Vaccinerade tidsserie dos 5' tabs of the [FoHM data file](https://blobserver.dc.scilifelab.se/blob/Folkhalsomyndigheten_Covid19_Vaccine-93.xlsx). These tabs contained data about the amount of individuals that received at least one or two doses, at least 3 doses, at least 4 doses, and at least 5 doses, respectively. For the 'whole population method', we use the latest population data from [Statistics Sweden (SCB)](https://www.scb.se/) and the most recent 'raw number' of the doses administered from same tabs in the [FoHM data file](https://blobserver.dc.scilifelab.se/blob/Folkhalsomyndigheten_Covid19_Vaccine-93.xlsx).
 
 **Note on the graph:** Click on the coloured squares in the legend of the below graph to toggle which datasets are displayed. A single click will toggle just that dataset on/off. It is possible to display only one of the datasets by double-clicking on the desired dataset.
 
@@ -83,7 +83,7 @@ To summarise, in total, <span id="eligible_one_dose"></span>% of the population
 
 In Sweden, the first vaccine doses were administered in early 2021. As in other countries, the first two doses were made available to progressively younger age groups over time. The third dose of the vaccine was first offered in autumn of 2021, and was offered to individuals in particular ages groups at a given interval after their second dose. The age group and interval length differed over time, with age groups generally getting younger and the interval becoming shorter. A third dose is not offered to those under 18 years of age, unless there are additional considerations e.g. the individual is immunocompromised. In early 2022, a fourth dose was made available to those aged over 80, those receiving care, those living in housing facilities for the elderly, and those with severe immunodeficiency. This was extended to include those over 65 in April 2022. As of September 2022, it was made largely available to those over 18, though the availability varied between counties. At each stage of the rollout of the fourth dose, exceptions were made so that others could get the fourth dose under specific circumstances, for example, where an individual is immunocompromised or taking care of a vulnerable individual. A fifth dose was made available to those over 65 in September 2022 and, as with the other doses, it is likely to be made available to more of the population over time and other groups are able to access it under certain conditions.
 
-Time series data is available in different tabs of the [FoHM data file](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data). We therefore took data from different places to produce the below time series. Time series data related to the amount of individuals that have received at least one or two doses is available in the 'Vaccinerade tidsserie' tab. Time series data about the amount of individuals that have at least 3, 4, or 5 doses is available in the 'Vaccinerade tidsserie dos 3', 'Vaccinerade tidsserie dos 4', and 'Vaccinerade tidsserie dos 5' tabs, respectively. Again, please note that it would not be appropriate to compare across all of the dose levels, both because the vaccines are not similarly available and because FoHM do not include all of the doses administered in their data. Firstly, a dose is only 'counted' in the FoHM data if it is administered to an individual within a specific age range. Data on the first on second doses is only included for individuals born in or before 2010 (around 12 years old). Data on the third and fourth doses is only included for individuals born in or before 2004 (around 18 years old). Data on the fifth dose is only included if it was given to an individual born in or before 1957 (around 65 years old). There are also some other caveats about whether a dose is 'counted' in the data file. In particular, data on the third dose is only included if it was registered after 1st September 2021 and at least 8 weeks after the individual received their second dose. Similarly, data on the fourth dose is only included if it was registered after 21st January 2022 and at least 8 weeks after the individual received their third dose. Lastly, data on dose 5 is only included if the dose was registerd after 15th August 2022 and was received at least 80 days after the individual received dose 4.
+Time series data is available in different tabs of the [FoHM data file](https://blobserver.dc.scilifelab.se/blob/Folkhalsomyndigheten_Covid19_Vaccine-93.xlsx). We therefore took data from different places to produce the below time series. Time series data related to the amount of individuals that have received at least one or two doses is available in the 'Vaccinerade tidsserie' tab. Time series data about the amount of individuals that have at least 3, 4, or 5 doses is available in the 'Vaccinerade tidsserie dos 3', 'Vaccinerade tidsserie dos 4', and 'Vaccinerade tidsserie dos 5' tabs, respectively. Again, please note that it would not be appropriate to compare across all of the dose levels, both because the vaccines are not similarly available and because FoHM do not include all of the doses administered in their data. Firstly, a dose is only 'counted' in the FoHM data if it is administered to an individual within a specific age range. Data on the first on second doses is only included for individuals born in or before 2010 (around 12 years old). Data on the third and fourth doses is only included for individuals born in or before 2004 (around 18 years old). Data on the fifth dose is only included if it was given to an individual born in or before 1957 (around 65 years old). There are also some other caveats about whether a dose is 'counted' in the data file. In particular, data on the third dose is only included if it was registered after 1st September 2021 and at least 8 weeks after the individual received their second dose. Similarly, data on the fourth dose is only included if it was registered after 21st January 2022 and at least 8 weeks after the individual received their third dose. Lastly, data on dose 5 is only included if the dose was registerd after 15th August 2022 and was received at least 80 days after the individual received dose 4.
 
 The below graph shows vaccine coverage across the whole of Sweden. We use the 'whole population' method for calculation, as this is more often used by other countries. Our calculations will therefore differ from the percentage values provided by FoHM as part of their summary statistics, because they use the 'eligible population' method of calculation. For more details on the two methods, see the [general summary statistics](/dashboards/vaccines/#general-summary-statistics) section.
 
@@ -97,7 +97,7 @@ The below graph shows vaccine coverage across the whole of Sweden. We use the 'w
 
 ### Administration of vaccinations in each Swedish county (län)
 
-In this section, we explore how many individuals in a given Swedish county (län) had at least X vaccine doses. Here, we again use the 'whole population' method of calculation (see the [general summary statistics](/dashboards/vaccines/#general-summary-statistics) section for details). Data on the total number of people in each county was taken from [Statistics Sweden (SCB)](https://www.scb.se/en/finding-statistics/statistics-by-subject-area/population/population-composition/population-statistics/). Data on the amount of individuals given at least one or two doses in each county was taken from the 'Vaccinerade tidsserie' tab of the [data from FoHM](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data). As mentioned in previous sections, only doses given to individuals born in or before 2010 (around 12 years old) are counted. Data on the amount of individuals given at least 3 or 4 doses (available in the 'Vaccinerade tidsserie dos 3' and 'Vaccinerade tidsserie dos 4' tabs of the [FoHM data](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data), respectively) is only given for those born bore 2004 (around 18 years old) and in accordance with specific timeframes and registration timepoints. Data on the fifth dose (available in the 'Vaccinerade tidsserie dos 5' tab of the [FoHM data](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data)) is only available for those born before 1957 (around 65 years old), and in accordance with certain timeframes. Given the differences in which data is 'counted' for each dose, it is clear that data should not be compared across doses.
+In this section, we explore how many individuals in a given Swedish county (län) had at least X vaccine doses. Here, we again use the 'whole population' method of calculation (see the [general summary statistics](/dashboards/vaccines/#general-summary-statistics) section for details). Data on the total number of people in each county was taken from [Statistics Sweden (SCB)](https://www.scb.se/en/finding-statistics/statistics-by-subject-area/population/population-composition/population-statistics/). Data on the amount of individuals given at least one or two doses in each county was taken from the 'Vaccinerade tidsserie' tab of the [data from FoHM](https://blobserver.dc.scilifelab.se/blob/Folkhalsomyndigheten_Covid19_Vaccine-93.xlsx). As mentioned in previous sections, only doses given to individuals born in or before 2010 (around 12 years old) are counted. Data on the amount of individuals given at least 3 or 4 doses (available in the 'Vaccinerade tidsserie dos 3' and 'Vaccinerade tidsserie dos 4' tabs of the [FoHM data](https://blobserver.dc.scilifelab.se/blob/Folkhalsomyndigheten_Covid19_Vaccine-93.xlsx), respectively) is only given for those born before 2004 (around 18 years old) and in accordance with specific timeframes and registration timepoints. Data on the fifth dose (available in the 'Vaccinerade tidsserie dos 5' tab of the [FoHM data](https://blobserver.dc.scilifelab.se/blob/Folkhalsomyndigheten_Covid19_Vaccine-93.xlsx)) is only available for those born before 1957 (around 65 years old), and in accordance with certain timeframes. Given the differences in which data is 'counted' for each dose, it is clear that data should not be compared across doses.
 
 As data for the fifth dose is available to such a small amount of the population, we have decided to analyse the data using both the 'whole population' and 'eligible population' methods. We feel that this will allow a clearer understanding of the differences between län in terms of the coverage for the fourth dose.
 
@@ -154,7 +154,7 @@ Please note the differences between the two below maps. Coverage appears to be v
 
 The below heatmap provides some indication of the vaccine coverage across different age groups. The data for this **heatmap differs from that in the previous visualisations**. Specifically, instead of showing the number of people with 'at least X doses', the heatmap shows the number of people in Sweden in each age group that have been given **that specific number of doses**. For example, rather than showing the amount of people with 'at least one dose', we show the number that have had 'only one dose'. Understandably, the number that have received ONLY one dose is relatively low across all age groups; individuals that have taken one dose are naturally more likely to take subsequent doses when they become eligible to do so. Given that individuals in more advanced age categories are eligible to take more doses, coverage is likely to be higher at a greater dose level. Age groups that have only recently become eligible for a given dose level are likely to initially show low coverage.
 
-The fact that data is not available for each age category for every dose is reflected in the graph (a white colouration is used to indicate where data is not available/included). Data on the first three doses are available in the 'Dos 1 till 3 per åldersgrupp' tab of the [FoHM dataset](https://fohm.maps.arcgis.com/sharing/rest/content/items/fc749115877443d29c2a49ea9eca77e9/data)). Data on the fourth and fifth doses are instead available in the 'Dos 4 18+' and 'Dos 5 per åldersgrupp' tabs, respectively.
+The fact that data is not available for each age category for every dose is reflected in the graph (a white colouration is used to indicate where data is not available/included). Data on the first three doses are available in the 'Dos 1 till 3 per åldersgrupp' tab of the [FoHM dataset](https://blobserver.dc.scilifelab.se/blob/Folkhalsomyndigheten_Covid19_Vaccine-93.xlsx). Data on the fourth and fifth doses are instead available in the 'Dos 4 18+' and 'Dos 5 per åldersgrupp' tabs, respectively.
 
 The 'eligible population method' was used in this case, as it would not be appropriate to consider the whole population when considering vaccination coverage within specific age groups.