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Merge pull request #1144 from ScilifelabDataCentre/FREYA-725/Abdullah
Updated plots of NPC statistics from vega to plotly
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@@ -4,12 +4,13 @@ description: The national Pandemic Centre (NPC) conducted testing related to SAR | |
| banner: /dashboard_thumbs/NPC_logo.png | ||
| banner_border: true | ||
| menu: | ||
| dashboard_menu: | ||
| identifier: npc-statistics | ||
| name: "National Pandemic Centre (Historic)" | ||
| dashboard_menu: | ||
| identifier: npc-statistics | ||
| name: "SARS-CoV-2 tests at National Pandemic Centre" | ||
| toc: false | ||
| plotly: true | ||
| aliases: | ||
| - /data_types/health_data/npc-statistics/ | ||
| - /data_types/health_data/npc-statistics/ | ||
| dashboards_topics: [COVID-19, Infectious diseases] | ||
| --- | ||
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@@ -19,131 +20,94 @@ dashboards_topics: [COVID-19, Infectious diseases] | |
| <a class="dark-blue" href="https://nyheter.ki.se/covid-19-tester-ki-atergar-till-ordinarie-laboratorieverksamhet-men-har-fortsatt-beredskap">KI Press Release</a> | ||
| </div> | ||
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||
| The dataset visualised in the graphs on this page is available [here](https://datagraphics.dc.scilifelab.se/dataset/bbbaf64a25a1452287a8630503f07418). The numbers reported here were compiled automatically and, as such, might not correspond to | ||
| the numbers reported through other sources for different reasons. | ||
| The dataset visualised in the graphs on this page is available [on SciLifeLab's Blobserver](https://blobserver.dc.scilifelab.se/blob/NPC-statistics-data-set.csv). The numbers reported here were compiled automatically and, as such, might not correspond to the numbers reported through other sources for different reasons. | ||
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| #### Total NPC test numbers | ||
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| The total number of SARS-CoV-2 (COVID-19) tests conducted at the national Pandemic Centre (NPC) since the start of the pandemic, separated according to whether the results were positive, negative, or invalid/inconclusive. | ||
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| Source code for the below graph is available [here](https://datagraphics.dc.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1). | ||
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| <div class="d-lg-none alert alert-info"> | ||
| Scroll the plot sideways to view all data. | ||
| <div class="d-md-none alert alert-info"> | ||
| Rotating your phone may improve graph layout | ||
| </div> | ||
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| <div class="plot_wrapper"> | ||
| <div class="w-100" id="total-numbers-chart"></div> | ||
| <div class="plot_wrapper mb-3"> | ||
| <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_total_tests.json" height="200px">}}</div> | ||
| </div> | ||
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| **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_total_tests.py). | ||
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| #### NPC test numbers | ||
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| The number of SARS-CoV-2 (COVID-19) tests ran daily or weekly, divided according to whether results were positive, negative, or invalid/inconclusive. | ||
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| Source code is available for both the [daily](https://datagraphics.dc.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc) and [weekly](https://datagraphics.dc.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf) graphs below. | ||
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| <div id="dwbuttons"><button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#daily_stacked_bar_chart" aria-expanded="true" aria-controls="#daily_stacked_bar_chart"> | ||
| Daily | ||
| </button> | ||
| </div> | ||
| <div class="collapse show" id="daily_stacked_bar_chart"> | ||
| <div class="d-lg-none alert alert-info"> | ||
| Scroll the plot sideways to view all data. | ||
| </div> | ||
| <div class="plot_wrapper"> | ||
| <div class="w-100" id="stacked-bar-chart"></div> | ||
| </div> | ||
| ##### Daily | ||
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||
| <div class="d-md-none alert alert-info"> | ||
| Rotating your phone may improve graph layout | ||
| </div> | ||
| <div id="dwbuttons"> | ||
| <button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#weekly_stacked_bar_chart" aria-expanded="true" aria-controls="weekly_stacked_bar_chart"> | ||
| Weekly | ||
| </button></div> | ||
| <div class="collapse show" id="weekly_stacked_bar_chart"> | ||
| <div class="d-lg-none alert alert-info"> | ||
| Scroll the plot sideways to view all data. | ||
| </div> | ||
| <div class="plot_wrapper"> | ||
| <div class="w-100" id="stacked-bar-chart-weekly"></div> | ||
| </div> | ||
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| <div class="plot_wrapper mb-3"> | ||
| <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_tests_daily.json" height="350px">}}</div> | ||
| </div> | ||
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| #### NPC tests positive fraction | ||
| **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_tests_daily.py). | ||
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| The fraction of daily or weekly SARS-CoV-2 (COVID-19) tests that were positive, | ||
| as percentage of all tests conducted (excluding invalid/inconclusive). | ||
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| Source code is available for both the [daily](https://datagraphics.dc.scilifelab.se/graphic/b31c50be59c84c93986c25b052115a65) and [weekly](https://datagraphics.dc.scilifelab.se/graphic/7f27ae237b8146a498ab4014aadc35db) graphs below. | ||
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| <div id="dwbuttons"><button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#daily_positive_bar_chart" aria-expanded="true" aria-controls="#daily_positive_bar_chart"> | ||
| Daily | ||
| </button></div> | ||
| <div class="collapse show" id="daily_positive_bar_chart"> | ||
| <div class="d-lg-none alert alert-info"> | ||
| Scroll the plot sideways to view all data. | ||
| </div> | ||
| <div class="plot_wrapper"> | ||
| <div class="w-100" id="positive-bar-chart"></div> | ||
| </div> | ||
| <p class="small"><i>*Note that as the number of reported analyses vary, some days may have a low number of samples, affecting the statistics a lot for that day, e.g. August 24th where only seven samples were reported, all positive.</i></p> | ||
| ##### Weekly | ||
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||
| <div class="d-md-none alert alert-info"> | ||
| Rotating your phone may improve graph layout | ||
| </div> | ||
| <div id="dwbuttons"><button class="btn btn-secondary" type="button" data-toggle="collapse" data-target="#weekly_positive_bar_chart" aria-expanded="true" aria-controls="weekly_positive_bar_chart"> | ||
| Weekly | ||
| </button></div> | ||
| <div class="collapse show" id="weekly_positive_bar_chart"> | ||
| <div class="d-lg-none alert alert-info"> | ||
| Scroll the plot sideways to view all data. | ||
| </div> | ||
| <div class="plot_wrapper"> | ||
| <div class="w-100" id="positive-bar-chart-weekly"></div> | ||
| </div> | ||
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| <div class="plot_wrapper mb-3"> | ||
| <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_tests_weekly.json" height="350px">}}</div> | ||
| </div> | ||
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| #### Cumulative NPC test numbers | ||
| **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_tests_weekly.py). | ||
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| The sum of all SARS-CoV-2 (COVID-19) virus tests conducted at NPC since the | ||
| start of the pandemic, as a function of date, and divided according to whether results were positive, negative, or invalid/inconclusive. | ||
| #### NPC tests positive fraction | ||
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| Source code for the below graph is available [here](https://datagraphics.dc.scilifelab.se/graphic/9145856246004419983d39fcf56d9eb6). | ||
| The fraction of daily or weekly SARS-CoV-2 (COVID-19) tests that were positive, | ||
| as percentage of all tests conducted **(excluding invalid/inconclusive)**. | ||
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| ##### Daily | ||
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||
| <div class="d-md-none alert alert-info"> | ||
| Rotating your phone may improve graph layout | ||
| </div> | ||
|
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||
| <div class="d-lg-none alert alert-info"> | ||
| Scroll the plot sideways to view all data. | ||
| <div class="plot_wrapper mb-3"> | ||
| <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_positiveTests_fraction_daily.json" height="350px">}}</div> | ||
| </div> | ||
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| <div class="plot_wrapper"> | ||
| <div class="w-100" id="cumulative-plot"></div> | ||
| **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_positiveTests_fraction_daily.py). | ||
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| ##### Weekly | ||
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| <div class="d-md-none alert alert-info"> | ||
| Rotating your phone may improve graph layout | ||
| </div> | ||
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| The National Pandemic Centre (NPC) was a facility for | ||
| [SARS-CoV-2 (COVID-19) testing](https://ki.se/mtc/ctmr-and-covid-19) | ||
| established within the | ||
| [Centre for Translational Microbiome Research (CTMR)](https://ki.se/en/research/centre-for-translational-microbiome-research-ctmr) | ||
| at | ||
| [Karolinska Institutet (KI)](https://ki.se/en)/[SciLifeLab](https://www.scilifelab.se/). | ||
| At the end of March 2020, the large-scale microbiome research lab was | ||
| quickly converted into a centre to assist Sweden with analysing | ||
| SARS-CoV-2 tests. This was made possible by a donation from the | ||
| [Knut and Alice Wallenberg Foundation (KAW)](https://kaw.wallenberg.org/en) and a previously established collaboration with | ||
| [MGI Tech](https://en.mgitech.cn/) in Shenzen, China. The NPC initially helped to expand the RNA-extraction capacity at Karolinska | ||
| Universitets laboratoriet. However, it quickly expanded into a facility that increased the testing capacity across all regions of Sweden. | ||
| <div class="plot_wrapper mb-3"> | ||
| <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_positiveTests_fraction_weekly.json" height="350px">}}</div> | ||
| </div> | ||
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| The final capacity of the National Pandemic Centre at KI/SciLifeLab | ||
| was approximately 10,000 tests per day. The results were typically | ||
| returned within 24 hours of the sample arriving to the lab. NPC | ||
| exclusively performed PCR-based analyses, not serological | ||
| (antibody-based) analyses. | ||
| **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_positiveTests_fraction_weekly.py). | ||
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| <script src="https://cdn.jsdelivr.net/npm/[email protected]"></script> | ||
| <script src="https://cdn.jsdelivr.net/npm/[email protected]"></script> | ||
| <script src="https://cdn.jsdelivr.net/npm/[email protected]"></script> | ||
| #### Cumulative NPC test numbers | ||
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||
| <script src="https://datagraphics.dc.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1.js?id=total-numbers-chart"></script> | ||
| The sum of all SARS-CoV-2 (COVID-19) virus tests conducted at NPC since the | ||
| start of the pandemic, as a function of date, and divided according to whether results were positive, negative, or invalid/inconclusive. | ||
|
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||
| <script src="https://datagraphics.dc.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc.js?id=stacked-bar-chart"></script> | ||
| <div class="d-md-none alert alert-info"> | ||
| Rotating your phone may improve graph layout | ||
| </div> | ||
|
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| <script src="https://datagraphics.dc.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf.js?id=stacked-bar-chart-weekly"></script> | ||
| <div class="plot_wrapper mb-3"> | ||
| <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/npc_cumulative_tests.json" height="550px">}}</div> | ||
| </div> | ||
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| <script src="https://datagraphics.dc.scilifelab.se/graphic/b31c50be59c84c93986c25b052115a65.js?id=positive-bar-chart"></script> | ||
| **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/pathogens-portal-visualisations/blob/main/npctests/npc_cumulative_tests.py). | ||
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| <script src="https://datagraphics.dc.scilifelab.se/graphic/9145856246004419983d39fcf56d9eb6.js?id=cumulative-plot"></script> | ||
| The National Pandemic Centre (NPC) was a facility for [SARS-CoV-2 (COVID-19) testing](https://ki.se/mtc/ctmr-and-covid-19) established within the [Centre for Translational Microbiome Research (CTMR)](https://ki.se/en/research/centre-for-translational-microbiome-research-ctmr) at [Karolinska Institutet (KI)](https://ki.se/en)/[SciLifeLab](https://www.scilifelab.se/). At the end of March 2020, the large-scale microbiome research lab was quickly converted into a centre to assist Sweden with analysing SARS-CoV-2 tests. This was made possible by a donation from the [Knut and Alice Wallenberg Foundation (KAW)](https://kaw.wallenberg.org/en) and a previously established collaboration with [MGI Tech](https://en.mgitech.cn/) in Shenzen, China. The NPC initially helped to expand the RNA-extraction capacity at Karolinska Universitets laboratoriet. However, it quickly expanded into a facility that increased the testing capacity across all regions of Sweden. | ||
|
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| <script src="https://datagraphics.dc.scilifelab.se/graphic/7f27ae237b8146a498ab4014aadc35db.js?id=positive-bar-chart-weekly"></script> | ||
| The final capacity of the National Pandemic Centre at KI/SciLifeLab was approximately 10,000 tests per day. The results were typically returned within 24 hours of the sample arriving to the lab. NPC exclusively performed PCR-based analyses, not serological (antibody-based) analyses. | ||
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