Merge pull request #1035 from ScilifelabDataCentre/mobile_notes

Mobile notes

content/english/dashboards/RECOVAC.md

@@ -89,6 +89,10 @@ When hovering over the plot with the cursor, additional grey icons appear in the
   </div>
 </div>
 
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
+</div>
+
 <div class="plot_wrapper mb-3">
   <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/swedishpop_subplot_button.json" height="800px" >}}</div>
 </div>
@@ -139,6 +143,10 @@ When hovering over the plot with the cursor, additional grey icons appear in the
   </div>
 </div>
 
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
+</div>
+
 <div class="plot_wrapper mb-3">
   <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/comorbs_subplot_button.json" height="800px" >}}</div>
 </div>

content/english/dashboards/covid_publications.md

@@ -5,20 +5,25 @@ banner: /dashboard_thumbs/publications.jpg
 toc: false
 plotly: true
 menu:
-    dashboard_menu:
-        identifier: covid_19_publications_vis
-        name: "COVID-19 publication overview"
+  dashboard_menu:
+    identifier: covid_19_publications_vis
+    name: "COVID-19 publication overview"
 aliases:
-    - /projects/dashboard/
+  - /projects/dashboard/
 dashboards_topics: [COVID-19, Infectious diseases]
 ---
+
 The visualisations on this page evaluate the development of COVID-19 and SARS-CoV-2 research across Sweden by assessing publication output. Specifically, we consider multiple aspects of journal publications and preprints where at least one author has an affiliation with a Swedish research institute. The database containing the publications themselves [can be found on this page](/publications/). Note that our database is manually curated and, as such, may not be exhaustive. The full database is available for download and use for other purposes, please see [DOI: 10.17044/scilifelab.14124014](https://doi.org/10.17044/scilifelab.14124014) for details.
 
 The code used to produce the visulations on this page can be found on [GitHub](https://github.com/ScilifelabDataCentre/covid-portal-visualisations). Specifically, code related to the number of publications can be found in the ['Count_publications' folder of the repository](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Count_publications), and code used to generated the wordclouds can be found in the ['Wordcloud' folder](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/tree/main/Wordcloud).
 
 ## Number of new publications
 
-This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated daily, though the publications database is not.
+This graph displays the number of publications (including both journal publications and preprints) published each month, as well as the cumulative daily total of publications contained in the database. The dates reflect either the preprint upload date or the official journal publication date, whichever is the most recent. Where a given day of publication is not specified in the publication/upload date, we assign the date as the first of the month. This causes the appearance of a relatively sharp increase at the start of each month. This chart is updated weekly, though the publications database is not.
+
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
+</div>
 
 <div class="table-responsive">
 {{< publications_per_month >}}

content/english/dashboards/vaccines.md

@@ -5,11 +5,11 @@ banner: /dashboard_thumbs/vaccines.jpg
 toc: true
 plotly: true
 menu:
-    dashboard_menu:
-        identifier: vaccines
-        name: "Vaccine administration: COVID-19"
+  dashboard_menu:
+    identifier: vaccines
+    name: "Vaccine administration: COVID-19"
 aliases:
-    - /data_types/health_data/vaccines/
+  - /data_types/health_data/vaccines/
 dashboards_topics: [COVID-19, Infectious diseases]
 ---
 
@@ -77,7 +77,7 @@ Vaccination data is spread between multiple tabs of the [FoHM data file](https:/
 
 **Code used to generate the 'live text' in the summary paragraph below:** ['Live text' script](https://github.com/ScilifelabDataCentre/covid-portal-visualisations/blob/main/Vaccine_page/vaccine_livetext.py).
 
-To summarise, in total, <span id="eligible_one_dose"></span>% of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents <span id="population_one_dose"></span>% of the whole population. The values indicate that <span id="eligible_one_dose_lastweek"></span>% of the eligible population were vaccinated last week (a change in rate of <span id="eligible_one_dose_rate_change"></span>% compared to the previous week), or <span id="population_one_dose_lastweek"></span>% of the whole population (a change of <span id="population_one_dose_rate_change"></span>% compared to the previous week). By contrast, <span id="eligible_two_doses"></span>% of those eligible, and <span id="population_two_doses"></span>% of the whole population have received at least two doses in total. The values indicate that <span id="eligible_two_doses_lastweek"></span>% of those eligible and <span id="population_two_doses_lastweek"></span>% of the whole population received their second dose last week (a change in rate of <span id="eligible_two_doses_rate_change"></span>% and <span id="population_two_doses_rate_change"></span>% compared to the previous week, respectively). In total, <span id="eligible_three_doses"></span>% of the eligible population received the third dose, representing <span id="population_three_doses"></span>% of the whole population. This means that <span id="eligible_three_doses_lastweek"></span>% of the eligible population received their third dose last week (a change in rate of <span id="eligible_three_doses_rate_change"></span>% compared to the previous week), or <span id="population_three_doses_lastweek"></span>% of the whole population (a change of <span id="population_three_doses_rate_change"></span>% compared to the previous week). To date, <span id="population_four_doses"></span>% of the whole population has received a fourth dose, and <span id="eligible_four_doses"></span>% of those eligible. In the last week, <span id="population_four_doses_lastweek"></span>% of the whole population were vaccinated with a fourth dose, a change in rate of <span id="population_four_doses_rate_change"></span>% compared to the previous week. By contast, <span id="eligible_four_doses_lastweek"></span>% of the eligible population were vaccinated with a fourth dose, a relative change in rate of <span id="eligible_four_doses_rate_change"></span>% compared to the previous week. A fifth dose was added in September 2022, <span id="population_five_doses"></span>% of the Swedish population have received that dose to date, which amounts to <span id="eligible_five_doses"></span>% of those eligible. A total of <span id="population_five_doses_lastweek"></span>% of the whole population were vaccinated with a fifth dose in the last week, a change of <span id="population_five_doses_rate_change"></span>% compared to the week before. When considering only the eligible population, <span id="eligible_five_doses_lastweek"></span>% were given a fifth dose last week,  which constitutes a relative change in rate of <span id="eligible_five_doses_rate_change"></span>% compared to the previous week.
+To summarise, in total, <span id="eligible_one_dose"></span>% of the population that are eligible for the first dose have received at least one dose of vaccination against COVID-19, which represents <span id="population_one_dose"></span>% of the whole population. The values indicate that <span id="eligible_one_dose_lastweek"></span>% of the eligible population were vaccinated last week (a change in rate of <span id="eligible_one_dose_rate_change"></span>% compared to the previous week), or <span id="population_one_dose_lastweek"></span>% of the whole population (a change of <span id="population_one_dose_rate_change"></span>% compared to the previous week). By contrast, <span id="eligible_two_doses"></span>% of those eligible, and <span id="population_two_doses"></span>% of the whole population have received at least two doses in total. The values indicate that <span id="eligible_two_doses_lastweek"></span>% of those eligible and <span id="population_two_doses_lastweek"></span>% of the whole population received their second dose last week (a change in rate of <span id="eligible_two_doses_rate_change"></span>% and <span id="population_two_doses_rate_change"></span>% compared to the previous week, respectively). In total, <span id="eligible_three_doses"></span>% of the eligible population received the third dose, representing <span id="population_three_doses"></span>% of the whole population. This means that <span id="eligible_three_doses_lastweek"></span>% of the eligible population received their third dose last week (a change in rate of <span id="eligible_three_doses_rate_change"></span>% compared to the previous week), or <span id="population_three_doses_lastweek"></span>% of the whole population (a change of <span id="population_three_doses_rate_change"></span>% compared to the previous week). To date, <span id="population_four_doses"></span>% of the whole population has received a fourth dose, and <span id="eligible_four_doses"></span>% of those eligible. In the last week, <span id="population_four_doses_lastweek"></span>% of the whole population were vaccinated with a fourth dose, a change in rate of <span id="population_four_doses_rate_change"></span>% compared to the previous week. By contast, <span id="eligible_four_doses_lastweek"></span>% of the eligible population were vaccinated with a fourth dose, a relative change in rate of <span id="eligible_four_doses_rate_change"></span>% compared to the previous week. A fifth dose was added in September 2022, <span id="population_five_doses"></span>% of the Swedish population have received that dose to date, which amounts to <span id="eligible_five_doses"></span>% of those eligible. A total of <span id="population_five_doses_lastweek"></span>% of the whole population were vaccinated with a fifth dose in the last week, a change of <span id="population_five_doses_rate_change"></span>% compared to the week before. When considering only the eligible population, <span id="eligible_five_doses_lastweek"></span>% were given a fifth dose last week, which constitutes a relative change in rate of <span id="eligible_five_doses_rate_change"></span>% compared to the previous week.
 
 ### Administration of vaccinations over time
 

content/english/dashboards/wastewater/covid_quantification/covid_quant_GU.md

@@ -2,7 +2,7 @@
 title: Amount of SARS-CoV-2 in wastewater (GU)
 plotly: true
 aliases:
-    - /dashboards/wastewater/covid_quant_gu/
+  - /dashboards/wastewater/covid_quant_gu/
 ---
 
 <div class="mt-3">
@@ -18,13 +18,13 @@ The data and visualisation on this page are usually updated weekly.
 
 ## Wastewater collection sites
 
-Influent wastewater samples were collected from Ryaverket wastewater treatment plant (WWTP) in Gothenburg. Wastewater sample collection began on February 10th (week 7) of 2020. Ryaverket WWTP receives wastewater from the households of more than 790,000 residents of Gothenburg, as well as from industry in the area. Wastewater is also received from residents and industry in surrounding municipalities, including Ale, Härryda, Kungälv, Lerum, Mölndal, and Partille, as well as storm and snow-melt water from older parts of Gothenburg. The amount of wastewater from households remains relatively consistent throughout the year. However, the amount of wastewater overall can be affected by the weather (with higher precipitation resulting in greater amounts). More information about the sample location, sample week, volume, and influent wastewater flow, is available in [Wang *et al.* (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/).
+Influent wastewater samples were collected from Ryaverket wastewater treatment plant (WWTP) in Gothenburg. Wastewater sample collection began on February 10th (week 7) of 2020. Ryaverket WWTP receives wastewater from the households of more than 790,000 residents of Gothenburg, as well as from industry in the area. Wastewater is also received from residents and industry in surrounding municipalities, including Ale, Härryda, Kungälv, Lerum, Mölndal, and Partille, as well as storm and snow-melt water from older parts of Gothenburg. The amount of wastewater from households remains relatively consistent throughout the year. However, the amount of wastewater overall can be affected by the weather (with higher precipitation resulting in greater amounts). More information about the sample location, sample week, volume, and influent wastewater flow, is available in [Wang _et al._ (2022)](https://pubmed.ncbi.nlm.nih.gov/36035197/).
 
 ## Visualisations
 
 <div class="alert alert-info">Last updated: <span id="last_modified_gu"></span></div>
 
-*The blue block on the graph indicates the period where sample collection was not completed (week 45 2022 - week 2 2023).*
+_The blue block on the graph indicates the period where sample collection was not completed (week 45 2022 - week 2 2023)._
 
 <!-- <button type="button" class="btn btn-sm btn-outline-secondary mb-2" data-bs-toggle="modal" data-bs-target="#interactiveFeaturesModal">
   How to use the interactive features of the plot
@@ -55,6 +55,10 @@ Influent wastewater samples were collected from Ryaverket wastewater treatment p
   </div>
 </div> -->
 
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
+</div>
+
  <div class="plot_wrapper mb-3">
   <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_gothenburg.json" height="550px" >}}</div>
 </div>
@@ -72,7 +76,7 @@ Influent wastewater samples were collected from Ryaverket wastewater treatment p
 **Download the data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://blobserver.dc.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx). Results are available for SARS-CoV-2 from week 7 of 2020 (with a small gap over winter 2022-2023), and for enteric viruses from week 2 of 2023. Updated weekly.\
 **Contact:** <[email protected]>
 
-**How to cite the dataset:**  Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501).
+**How to cite the dataset:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501).
 
 **How to cite method:**
 Saguti, F., Magnil, E., Enache, L., Churqui, M.P., Johansson, A., Lumley, D., Davidsson, F., Dotevall, L., Mattsson, A., Trybala, E., Lagging, M., Lindh, M., Gisslen, M., Brezicka, T., Nystrom, K. and Norder, H. (2021). Surveillance of wastewater revealed peaks of SARS-CoV-2 preceding those of hospitalized patients with COVID-19. [https://doi.org/10.1016/j.watres.2020.116620](https://doi.org/10.1016/j.watres.2020.116620).
@@ -83,7 +87,7 @@ Wang, H., Churqui, M.P., Tunovic, T., Enache, L., Johansson, A., Karmander, A.,
 
 Samples of wastewater were collected using a fixed-site sampler that collected 30ml per 10,000m<sup>3</sup> of the incoming wastewater. For the purposes of analysis, seven samples (each representing a 24 hour period) were pooled to create a weekly sample. The weekly sample, which consisted of 1.5-15l of wastewater (depending on the flow) was sent to the Clinical Microbiology Laboratory at Sahlgrenska University Hospital for analysis. Analyses were conducted on the Monday after the sample was collected.
 
-At the Clinical Microbiology Laboratory, viruses were concentrated to a final volume of 2.5ml, using a method that was developed in-house. This method uses the NanoCeram electropositive filter (Argonide, Florida, USA) as the primary means of concentration, and then ultracentrifugation as secondary concentration method ([Saguti *et al.*, 2021](https://pubmed.ncbi.nlm.nih.gov/33212338/)). Nucleic acids were extracted from 1ml of the concentrated sample using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Real-time quantitative PCR (RT-qPCR) was performed to detect the RNA-dependent RNA polymerase (RdRP) region of SARS-CoV-2. In all runs, a 10-fold serial diluted plasmid (Eurofins Genomics, Ebersberg, Germany) that contained the target SARS-CoV-2 region was used as a positive control. Nuclease-free water was used as a negative control. The Ct values from the qPCR were used to quantify the amount of SARS-CoV-2 genome in the sample. Details about the method of calculation are provided in [Saguti *et al.* (2021)](https://pubmed.ncbi.nlm.nih.gov/33212338/). The relative amount of viral genome in the wastewater was calculated by dividing the amount of viral genome in the sample by the amount of SARS-CoV-2 genome in the incoming wastewater during week 11 (mid-March) of 2020. Samples from all subsequent weeks contained detectable SARS-CoV-2 genome.
+At the Clinical Microbiology Laboratory, viruses were concentrated to a final volume of 2.5ml, using a method that was developed in-house. This method uses the NanoCeram electropositive filter (Argonide, Florida, USA) as the primary means of concentration, and then ultracentrifugation as secondary concentration method ([Saguti _et al._, 2021](https://pubmed.ncbi.nlm.nih.gov/33212338/)). Nucleic acids were extracted from 1ml of the concentrated sample using the QIAamp Circulating Nucleic Acid Kit (Qiagen, Hilden, Germany). Real-time quantitative PCR (RT-qPCR) was performed to detect the RNA-dependent RNA polymerase (RdRP) region of SARS-CoV-2. In all runs, a 10-fold serial diluted plasmid (Eurofins Genomics, Ebersberg, Germany) that contained the target SARS-CoV-2 region was used as a positive control. Nuclease-free water was used as a negative control. The Ct values from the qPCR were used to quantify the amount of SARS-CoV-2 genome in the sample. Details about the method of calculation are provided in [Saguti _et al._ (2021)](https://pubmed.ncbi.nlm.nih.gov/33212338/). The relative amount of viral genome in the wastewater was calculated by dividing the amount of viral genome in the sample by the amount of SARS-CoV-2 genome in the incoming wastewater during week 11 (mid-March) of 2020. Samples from all subsequent weeks contained detectable SARS-CoV-2 genome.
 
 <br>
 <div class="mt-3">

content/english/dashboards/wastewater/covid_quantification/covid_quant_KTH.md

@@ -65,6 +65,10 @@ Please also note that although the same methods are used for all cities shown on
   </div>
 </div>
 
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
+</div>
+
 <div class="plot_wrapper mb-3">
   <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_stockholm.json" height="550px" >}}</div>
 </div>
@@ -76,7 +80,7 @@ Please also note that although the same methods are used for all cities shown on
 <div class="alert alert-info">Last updated: <span id="last_modified_malmo"></span></div>
 
 <div class="d-md-none alert alert-info">
-  Scroll the plot sideways to view all data.
+  Rotating your phone may improve graph layout
 </div>
 
 <div class="plot_wrapper mb-3">

content/english/dashboards/wastewater/covid_quantification/covid_quant_SLU.md

@@ -65,6 +65,10 @@ Please note that although the same methods are used for all cities shown on this
   </div>
 </div>
 
+<div class="d-md-none alert alert-info">
+  Rotating your phone may improve graph layout
+</div>
+
 <div class="plot_wrapper mb-3">
   <div class="table-responsive">{{< plotly json="https://blobserver.dc.scilifelab.se/blob/wastewater_combined_slu_regular.json" height="600px" >}}</div>
 </div>