Merge pull request #988 from ScilifelabDataCentre/blob_crush

Crush covid text update and blob url fix

content/english/dashboards/RECOVAC.md

@@ -85,11 +85,11 @@ When hovering over the plot with the cursor, additional grey icons appear in the
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/vaccination_RECO_timeseries_buttons.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/vaccination_RECO_timeseries_buttons.json" height="500px" >}}</div>
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/ICUadmiss_vaccinationlevel_button.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/ICUadmiss_vaccinationlevel_button.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plots:** [Preparation for vaccine coverage data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_dataprep.py), [Graph of vaccine coverage](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_vaccinecov_plotwbuttons.py), [Graph and data preparation for ICU admissions data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/Swedishpop_ICU_plotwbuttons.py).
@@ -132,7 +132,7 @@ When hovering over the plot with the cursor, additional grey icons appear in the
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/comorbs_subplot_button.json" height="800px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/comorbs_subplot_button.json" height="800px" >}}</div>
 </div>
 
 **Code used to produce plots:** [Preparation of COVID-19 case data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_cases_dataprep.py), [Preparation of vaccination coverage data](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_vaccinecov_dataprep.py), [Graph containing subplots](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/RECOVAC/comorbidity_subplots_wbuttons.py).

content/english/dashboards/covid_publications.md

@@ -42,13 +42,13 @@ These wordclouds display the words and two word phrases that appear most frequen
 
 #### All publications
 
-<div class="row my-4"><div class="col-md-8"><img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-titles_all.png"></div></div>
+<div class="row my-4"><div class="col-md-8"><img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-titles_all.png"></div></div>
 
 #### Publications attributed to particular research funders
 
 Wordclouds are displayed for each funder that we identified as having been associated with at least 20 publications in the database.
 
-<div class="container"> <div class="row mt-2"> <div class="col-md mr-4"> <div class="row"> <h5>Swedish Research Council:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-titles_vr.png"> </div> </div> <div class="col-md mr-4"> <div class="row"> <h5>SciLifeLab/KAW:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-titles_kaw.png"> </div> </div> <div class="col-md"> <div class="row"> <h5>Horizon 2020:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-titles_h2020.png"> </div> </div> </div> </div>
+<div class="container"> <div class="row mt-2"> <div class="col-md mr-4"> <div class="row"> <h5>Swedish Research Council:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-titles_vr.png"> </div> </div> <div class="col-md mr-4"> <div class="row"> <h5>SciLifeLab/KAW:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-titles_kaw.png"> </div> </div> <div class="col-md"> <div class="row"> <h5>Horizon 2020:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-titles_h2020.png"> </div> </div> </div> </div>
 
 ## Most frequent words or two word phrases in the abstracts
 
@@ -58,10 +58,10 @@ These wordclouds display the words and two word phrases that appear most frequen
 
 #### All publications
 
-<div class="row my-4"><div class="col-md-8"><img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-abstracts_all.png"></div></div>
+<div class="row my-4"><div class="col-md-8"><img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-abstracts_all.png"></div></div>
 
 #### Publications attributed to particular research funders
 
 Wordclouds are displayed for each funder that we identified as having been associated with at least 20 publications in the database.
 
-<div class="container"> <div class="row mt-2"> <div class="col-md mr-4"> <div class="row"> <h5>Swedish Research Council:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-abstracts_vr.png"> </div> </div> <div class="col-md mr-4"> <div class="row"> <h5>SciLifeLab/KAW:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-abstracts_kaw.png"> </div> </div> <div class="col-md"> <div class="row"> <h5>Horizon 2020:</h5> </div> <div class="row"> <img src="https://blobserver.dckube.scilifelab.se/blob/covid-portal-abstracts_h2020.png"> </div> </div> </div> </div>
+<div class="container"> <div class="row mt-2"> <div class="col-md mr-4"> <div class="row"> <h5>Swedish Research Council:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-abstracts_vr.png"> </div> </div> <div class="col-md mr-4"> <div class="row"> <h5>SciLifeLab/KAW:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-abstracts_kaw.png"> </div> </div> <div class="col-md"> <div class="row"> <h5>Horizon 2020:</h5> </div> <div class="row"> <img src="https://blobserver.dc.scilifelab.se/blob/covid-portal-abstracts_h2020.png"> </div> </div> </div> </div>

content/english/dashboards/crush_covid.md

@@ -4,26 +4,40 @@ description: CRUSH Covid maps outbreaks in Uppsala County by visualising the num
 banner: /dashboard_thumbs/CRUSH.png
 toc: false
 menu:
-    dashboard_menu:
-        identifier: crush_covid
-        name: "CRUSH Covid Uppsala (Partner)"
+  dashboard_menu:
+    identifier: crush_covid
+    name: "CRUSH Covid Uppsala (Partner)"
 aliases:
-    - /data_types/health_data/crush_covid/
+  - /data_types/health_data/crush_covid/
 dashboards_topics: [COVID-19, Infectious diseases]
 ---
 
-<div class="containter"><div class="row mr-2 mt-2"><div class="col-lg-9"><p><b>CRUSH Covid</b> is a collaboration between the Region Uppsala and researchers from five different departments at Uppsala University. The purpose of the project is to map outbreaks of COVID-19 in Uppsala County and attempt to mitigate their impact by keeping the public informed. Information on the CRUSH Covid dashboard was originally updated weekly, but the update schedule changed in autumn 2022. The dashboard will now be <b>updated every 1-2 months.</b></p>
-<p>CRUSH Covid is led by Mats Martinell (senior lecturer at the Department of Public Health and Caring Sciences, General Medicine and Preventive Medicine, Uppsala University) and Tove Fall (professor of Molecular Epidemiology at the Department of Medical Sciences, Molecular Epidemiology, Uppsala University). Sewage analysis is supported by SciLifeLab and Uppsala Vatten. Modelling work is supported by Vinnova.</p>
-<p>For questions and feedback, please contact Georgios Varotsis (<a href="mailto:georgios.varotsis@medsci.uu.se">georgios.varotsis@medsci.uu.se</a>).</p><p>CRUSH Covid has received ethical approval from the Swedish Ethical Review Authority (ref. no. 2020-04210, 2020-06315 and 2020-06501).</p>
-</div><div class="col-lg-3"><div class="d-flex justify-content-center mb-3"><img src="/img/logos/crush_covid_logo.png" alt="CRUSH Covid" height="30"></div><div class="d-flex justify-content-center mb-3"><img src="/img/logos/uu_logo.png" alt="Uppsala University" height="100"></div>
-<div class="d-flex justify-content-center mb-3"><img src="/img/logos/regionuppsala_logo.png" alt="Region Uppsala" height="40"></div></div></div></div>
+<div class="containter">
+<div class="row mr-2 mt-2">
+<div class="col-lg-9">
+<p>CRUSH Covid Uppsala is a research project in which <b>Region Uppsala</b> collaborates with researchers from five different research departments at <b>Uppsala University</b>. The purpose of the project is to map outbreaks of COVID-19 in Uppsala County and to try to mitigate the impact of outbreaks by informing the public.</p>
+
+<p>CRUSH Covid is led by <b>Mats Martinell</b> (senior lecturer at the Department of Public Health and Caring Sciences, General Medicine and Preventive Medicine, Uppsala University) and <b>Tove Fall</b> (professor of Molecular Epidemiology at the Department of Medical Sciences, Molecular Epidemiology, Uppsala University). Sewage analysis is supported by SciLifeLab and Uppsala Vatten. Modelling work is supported by Vinnova.</p>
+
+<p>For questions and feedback, please contact <b>Georgios Varotsis</b> (<a href="mailto:georgios.varotsis@medsci.uu.se">georgios.varotsis@medsci.uu.se</a>).</p>
+
+<p>CRUSH Covid has received ethical approval from the Swedish Ethical Review Authority (ref. no. 2020-04210, 2020-06315 and 2020-06501).</p>
+
+<p>The CRUSH Covid team has released data and information about the project in two places. The primary source of data and information was their <a target="_blank" href="https://crush-covid.shinyapps.io/crush_covid/">custom shiny app, named the CRUSH Covid dashboard</a>, which contained data visualisations as well as reports. As of September 2022, updates to the app ceased. The Portal's dashboard (i.e. this webpage) is the secondary source of data and information for this project. The data generated from CRUSH Covid between 2020-2022 can be downloaded directly below.</p>
+</div>
+<div class="col-lg-3">
+<div class="d-flex justify-content-center mb-3"><img src="/img/logos/crush_covid_logo.png" alt="CRUSH Covid" height="30"></div>
+<div class="d-flex justify-content-center mb-3"><img src="/img/logos/uu_logo.png" alt="Uppsala University" height="100"></div>
+<div class="d-flex justify-content-center mb-3"><img src="/img/logos/regionuppsala_logo.png" alt="Region Uppsala" height="40"></div>
+</div>
+</div>
+</div>
 
 #### Download CRUSH Covid data
 
-<div class="alert alert-info">Last updated: {{% crush_covid_modified %}}.</div>
+<div class="alert alert-info">Last updated: 2022-09-15</div>
 
-* [Number of tests and % positivity by postal code in Uppsala County, .csv file](https://blobserver.dckube.scilifelab.se/blob/CRUSH_Covid_data.csv) (updated every 1-2 months from September 2022).
-    For each postal code which is found within the Uppsala län, the dataset contains weekly data on cases per capita, tests per capita and % positivity. Our estimates are calculated based on the adult population of each postal code (individuals 15 years of age and older). For reference, both the total population and the adult population are included.
+- [Number of tests and % positivity by postal code in Uppsala County, .csv file](https://blobserver.dc.scilifelab.se/blob/CRUSH_Covid_data.csv). For each postal code which is found within the Uppsala län, the dataset contains weekly data on cases per capita, tests per capita and % positivity. The estimates are calculated based on the adult population of each postal code (individuals 15 years of age and older). For reference, both the total population and the adult population are included.
 
 #### Interactive dashboard and reports
 

content/english/dashboards/post_covid.md

@@ -50,15 +50,15 @@ These plots display the number of times that patients were assigned the diagnose
 #### Diagnosis U09.9
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/U099_agesex_casedist.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_agesex_casedist.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py).
 
 #### Diagnosis Z86.1A/U08.9
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/U089_agesex_casedist.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_agesex_casedist.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/create_agesex_distcases.py).
@@ -70,15 +70,15 @@ The maps below show the number of people that received the diagnoses of interest
 #### Diagnosis U09.9
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/map_postcovid_percent_of_population_U099.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_population_U099.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Script to produce map](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U099.py).
 
 #### Diagnosis Z86.1A/U08.9
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/map_postcovid_percent_of_population_U089.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_population_U089.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Script to produce map](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_population_U089.py).
@@ -94,15 +94,15 @@ The maps below show the number of people that received the diagnoses of interest
 #### Diagnosis U09.9
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/map_postcovid_percent_of_covidcases_U099.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_covidcases_U099.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Script to produce map](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_cases_U099.py).
 
 #### Diagnosis Z86.1A/U08.9
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/map_postcovid_percent_of_covidcases_U089.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/map_postcovid_percent_of_covidcases_U089.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Data preparation script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_dataprep.py), [Script to produce map](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/postcovid_mapfig_cases_U089.py).
@@ -116,7 +116,7 @@ The maps below show the number of people that received the diagnoses of interest
 The below table displays the most common types of diagnosis (diagnosis groups) that have been reported together with the *U09.9 (ICD-10-SE) - Postinfectious state associated with COVID-19, unspecified* diagnosis. In particular, the values in the table represent the amount of individuals that received the *U09.9* diagnosis alongside one of the diagnoses below. The data was recorded between 16th October 2020 and the most recent data update (see above).
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/accompdiag_table.json" height="527px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/accompdiag_table.json" height="527px" >}}</div>
 </div>
 
 <span class="text-muted">*Note that an individual may have more than one of the accompanying diagnoses. However, if an individual has the same issue on multiple doctor visits/healthcare contacts, the diagnosis will only be counted once*</span>
@@ -132,7 +132,7 @@ The below plot shows the number of times that patients given the diagnoses of in
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/weeklycontacts_healthcare.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/weeklycontacts_healthcare.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare.py).
@@ -148,7 +148,7 @@ The below plots show the number of times that patients given one of the diagnose
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/U099_healthcare_divsex.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U099_healthcare_divsex.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py).
@@ -160,7 +160,7 @@ The below plots show the number of times that patients given one of the diagnose
 </div>
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/U089_healthcare_divsex.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/U089_healthcare_divsex.json" height="500px" >}}</div>
 </div>
 
 **Code used to produce plot:** [Script to produce plot](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/postCOVID/weeklycontacts_healthcare_divsex.py).

content/english/dashboards/symptom_study_sweden.md

@@ -26,7 +26,7 @@ COVID Symptom Study Sweden has two main objectives. The first objective is to in
 Below are estimates of the prevalence of symptomatic COVID-19 cases in various counties in Sweden. The estimates are made based on the app users' data using the prediction model developed by the team of researchers behind the COVID Symptoms Study Sweden; see [this page](https://www.covid19app.lu.se/artikel/uppdatering-av-prediktionsmodell-0) for more information about the prediction model (only available in Swedish). More detailed prevalence estimates and other results can be explored [on the official dashboard of the project results](https://csss-resultat.shinyapps.io/csss_dashboard/).
 
 <div class="plot_wrapper mb-3">
-  <div class="table-responsive">{{< plotly json="https://blobserver.dckube.scilifelab.se/blob/symptoms_map_english.json" height="500px" >}}</div>
+  <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/symptoms_map_english.json" height="500px" >}}</div>
 </div>
 
 #### Access to the collected data for use in other research projects