workshopF_2022.Rmd

---
title: 'BM424 workshop: infectious disease outbreak control'
author: "Morgan Feeney"
date: "06/12/2022"
output: 
  bookdown::html_document2:
    toc: true
    toc_float:
      toc_collapsed: false
    number_sections: false 
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
library(ggplot2)
library(knitr)

outbreak_deaths <- floor(runif(1, min = 10, max = 30))
city_name <- "Glenmarigg" 
hospital_name <- "Royal Jubilee" 
```

## Scenario F

Disaster has struck - hard on the heels of the COVID-19 pandemic, another disease outbreak has hit your fair city, `r city_name`. Residents are outraged and worried. There have already been `r outbreak_deaths` deaths.

The cause of the outbreak appears to be <i>Neisseria meningitidis</i>. (Please refer to the [CDC Meningococcal Disease Fact Sheet](https://www.cdc.gov/meningococcal/downloads/17-275138A-MeningococcalDis-FS.pdf) for more information about the disease.)

```{r Neisseria, out.width="50%", out.height="50%", echo=FALSE, fig.cap="Photomicrograph of Neisseria meningitidis diplococci. Image credit: [CDC](https://phil.cdc.gov/details.aspx?pid=6423)"}
knitr::include_graphics(rep("images/Neisseria.jpg"))
```

Each member of your group will play one of the following roles as you attempt to tackle the disease outbreak and save your city:

1.	Provost (head of the city council)
2.	Representative from a national public health org. (Public Health Scotland)
3.	Epidemiologist (on secondment from Public Health Scotland)
4.	Director of the city's main hospital (`r hospital_name`)
5.	City planner/civil servant
6.	Microbiologist (working in one of the NHS Scotland clinical labs)
7.	Public communications expert (past and current sci comm campaigns)
8.  Doctor at a major surgery in `r city_name`

You must work together, using the information that has been provided for you in the attached information packets, and decide what action(s) should be taken to control the outbreak currently plaguing your city, `r city_name`. Your actions should be evidence-based – use the peer-reviewed literature to decide on measures that will stop the pandemic in your scenario.

Your action points may include directives to gather more information (e.g., contact tracing of current cases, microbiological testing of food/water, etc.), or specific directives (e.g. public health measures, non-pharmaceutical interventions, etc.). Use the data/expertise of all group members. Be clear, concise, and specific.

You should submit 3-5 specific actions to control the pandemic, using the [workshop 3 pro forma](/proformas/BM424_workshop3_proforma.docx) (also available on MyPlace). Submit this by noon, Friday March 10th, via the submission link on MyPlace. 

***

## Information Packet F1

You are the provost of `r city_name`, elected in `r sample(2012:2021, size=1)`. 

```{r city, echo=FALSE, fig.cap="Photograph of Glenmarigg city centre. Image credit: DALL-E"}
knitr::include_graphics(rep("images/Glenmarigg.png"))
```


The current population of `r city_name` (as of December 2022) is `r sample(150000:170000, size=1)`. The demographic data for the city is shown below.

```{r A1, fig.show="hold", out.width="50%", echo=FALSE, fig.cap="Glenmarigg demographics (Source: Office for National Statistics)"}

Pop <- c(sample(150000:170000, size=3, replace=TRUE), sample(170000:180000, size=3, replace=TRUE), sample(190000:170000, size=2, replace=TRUE), sample(150000:170000, size=2, replace=TRUE))
PopYears <- c(2012:2021)
population <- data.frame(Pop, PopYears)
ggplot(data = population, aes(x=PopYears, y=Pop)) + 
  geom_point() +
  geom_line() +
  labs(y = "Number of Glenmarigg residents (estimated)", x = "Year") +
  scale_y_continuous(limits=c(0, 200000)) + 
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())


Demog <- c((rep("Births", 10)), (rep("Deaths", 10)))
Num <- c(sample(1000:2000, size=10, replace=TRUE), sample(500:1500, size=8, replace=TRUE), sample(3000:5500, size=2, replace=TRUE))
DemogYears <- c(rep(2012:2021, 2))
birthdeath <- data.frame(Demog, Num, DemogYears)
ggplot(data = birthdeath, aes(x=DemogYears, y=Num, group=Demog, colour=Demog)) + 
  geom_point() +
  geom_line() +
  labs(y = "Number of births and deaths in Glenmarigg (estimated)", x = "Year", colour = "Demographics") +
  scale_y_continuous(limits=c(0, 5500)) + 
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank()) + 
  scale_color_discrete(name="")
```
You were elected as a member of the popular "Community Change" party and made a number of election promises regarding a "Green New Deal" for `r city_name`.

```{r A2, fig.cap="Voting intention by Glenmarigg residents (Source: YouGov polling)", echo=FALSE}

Party <- c((rep("Moderate", 10)), (rep("Progress and Peace", 10)), (rep("Community Change", 10)), (rep("Aquamarine", 10)), (rep("Modern Union", 10)))
Polls <- c(sample(1:3, size=10, replace=TRUE), sample(8:14, size=10, replace=TRUE), sample(15:20, size=10, replace=TRUE), sample(5:10, size=10, replace=TRUE), sample(1:2, size=10, replace=TRUE))
PolYears <- c(rep(2012:2021, 5))
politics <- data.frame(Party, Polls, PolYears)
ggplot(data = politics, aes(x=PolYears, y=Polls, color=Party)) + 
  geom_point() +
  geom_line() +
  labs(y = "Voting Intention", x = "Year") + 
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())

Councillors <- sum(politics[politics$PolYears>2020, 2])
```

There are currently `r Councillors` elected councillors, representing the 5 main political parties in `r city_name` as follows:

```{r A3, echo=FALSE}

pol2021 <- (politics[politics$PolYears>2020, 2])
Parties <- c("Moderate", "Progress and Peace", "Community Change", "Aquamarine", "Modern Union")

Councillors <- data.frame(Parties, pol2021)

kable(x = Councillors, 
      format = "html", 
      col.names = c("Political Party", "Number of Seats"))

```
<br><br>
The overall budget (expenditures) for the 2021-2022 financial year is £`r sample(400000000:600000000, size=1)`. A summary of expeditures by category for this financial year is shown below. 

```{r A4, fig.cap="Public expenditures by category for the 2021-2022 financial year (Source: Glenmarigg City Council)", echo=FALSE}

expenses <- data.frame(
  Category=c("Education", "Industry and Agriculture", "Social Care", "Transport", "Public order and safety", "Healthcare", "Housing", "Other"),
  value=c(sample(8:15, size=1), sample(10:15, size=1), sample(4:10, size=1), sample(5:8, size=1), sample(5:9, size=1), sample(20:28, size=1), sample(7:15, size=1), sample(1:4, size=1))
)

ggplot(expenses, aes(x="", y=value, fill=Category)) +
  geom_bar(stat="identity", width=1, color="white") +
  coord_polar("y", start=0) +
  theme_void() 
```


```{r emails, echo=FALSE}

clos1 <- c("Yours sincerely,", "Best wishes,", "Kind regards,", "All the best,", "Sincerely,", "Yours truly,", "Respectfully,")
email1 <- c("gldk", "aptr", "bhr", "tgh", "pbr", "js", "lucy", "amd", "oirl", "jim", "ygg", "oli", "end", "lulu", "rye", "att")
adj1 <- c("Disgraceful", "Terrible", "Horrible", "Devastating", "Sad", "Bloody")
emotion1 <- c("outraged", "upset", "extremely vexed", "so angry", "devastated")
sent1 <- c("As if COVID wasn't enough! Has this city not suffered enough, I ask you.", "This seems to be too much to bear on top of COVID, the cost of living crisis, and the war in Ukraine. It is just one tragedy after another.", "Too many people have already died from COVID and it seems completely cruel to have another pandemic strike our city again so soon.", "There seems to be no end to the suffering that pandemics inflict on our city in these days.", "It seems almost like the apocalypse must be upon us, with this pandemic following so close upon the heels of COVID19.", "Too many people have died and it is such a tragedy.")
wish1 <- c("hope", "hope very much", "wish", "expect", "sincerely hope")
state1 <- c("dreadful state of affairs", "horrible pandemic", "all of the poor people dying", "tragedy")
time1 <- c("immediately", "very soon", "at once", "as soon as possible")
name1 <- c("Anna", "Luke", "Siobhan", "Su", "Ailidh", "Fiona", "Graham", "Madison", "Eleanor", "Rodrigo", "Kieran", "Wilson", "Anika", "Rosemary", "Alise", "Gordon", "Roman", "Karen")
verb1 <- c("devastate", "obliterate", "ruin", "destroy", "crush")
business1 <- c("small coffee shop", "coffee shop", "cafe", "restaurant", "bookshop", "boutique clothing store", "records shop", "used bookstore", "toy store", "sweet shop")
business2 <- c("The Glenmarigg Shop", "Fraser & Co.", "Bella's", "Around the Corner", "Jewels")
adj2 <- c("nearly", "almost", "virtually", "almost literally", "practically")
conseq1 <- c("lost my business due to those pandemic lockdowns", "had to close because of all the draconian lockdowns", "went out of business", "went bankrupt", "had to shut our doors during COVID")
sent2 <- c("I hope you realise how costly the last pandemic was for millions of people across the country, and that we can't afford another one.", "You should be ashamed to think of all the businesses that have had to close because of the coronavirus measures this city took, and all of the people who lost their jobs.", "Businesses must be free to operate, not prosecuted by some nanny state.", "Things are bad enough already with the cost of living crisis, war in Ukraine, and Brexit, we can't afford another pandemic.", "I hope you realise that you need to put businesses first now - we were unfairly forced to bear the costs of the last pandemic.", "I hope you realise how much business we have all lost in recent years, and how much businesses in this city are struggling financially.")
subj1 <- c("Government Overreach", "Government Overstep", "Stop This Madness", "New Pandemic Measures")
state2 <- c("awful pandemic", "terrible pandemic", "new crisis", "new pandemic", "new disease")
conseq2 <- c("another lockdown", "a return to COVID rules", "face masks and gallons of hand sanitizer", "the draconian lockdowns you imposed during COVID", "restrictions that cripple our businesses")
wish2 <- c("fear", "dread", "abhor the idea", "hate the idea", "am afraid")
sent3 <- c("This last pandemic was just a typical example of what governments do when given a little too much power.", "Machiavelli said that power corrupts absolutely, and he was absolutely right - look at what happened during the last pandemic.", "I am sick and tired of government interference with my life, I have the right to go about my life without some do-gooder from a public health agency telling me that I need to wear a mask and can't visit my grandmother.", "The mental health consequences of the last pandemic were underappreciated, but very real - people suffered due to the lockdowns and children's development was affected by the wearing of face masks and the closing of schools.")
sent4 <- c("Please do not use this disaster as another opportunity for oppressive lockdowns and government control of our lives.", "You must not allow the city to suffer through another round of lockdowns, face-masks, and other punitive restrictions that destroy people's lives.", "I hope that you will do the right thing in this time of crisis and that I will be able to vote for you again in the coming elections with a clean conscience.", "Facemasks are just the tyranny of the minority over the majority, I hope that you will not permit them again on your watch.")
subj2 <- c("This Terrible Tragedy", "Another Terrible Loss")
rel1 <- c("my mother-in-law", "my aunt", "my auntie", "my niece", "my nephew", "my husband's best friend", "my wife's best friend", "my sister-in-law", "my brother-in-law", "my uncle", "my granddad", "my gran", "my nana", "my nana's best friend")
sent5 <- c("The family are all devastated as you can surely imagine.", "Words cannot begin to describe our loss.", "This is truly a tragedy.", "This is an unspeakable loss.", "The family are all devastated by this loss.", "You cannot begin to imagine the grief that we are feeling.", "This is especially terrible coming hard on the heels of all of our losses due to COVID-19.")
sent6 <- c("I don't understand why we haven't learned how to deal with pandemics better, after all our experiences with COVID-19, I don't understand how this could have happened.", "I really wish that our government had better learned its lessons from the COVID-19 pandemic and could have prevented this terrible tragedy.", "I hope that, considering how many other families have also lost loved ones, that you and your office will be doing everything in their power to halt this pandemic and prevent more needless deaths.", "I hope that you will do everything you can to stop this pandemic so that no other families need to suffer this pain.", "I hope that you will do everything you can to stop this pandemic so that no more lives will be lost.", "I am sure that you and your office are doing your best, but I hope that in the fullness of time, there will be a public inquiry into how this pandemic was handled and why so many families have lost loved ones. Especially coming so soon after the lessons that we learned during the COVID-19 pandemic, I would have thought that this tragedy could have been prevented.")
```

Your office has recently received a great deal of correspondence regarding the pandemic in `r city_name`. A representative sample of these e-mails is shown below.

***
<b>From:</b> `r sample(email1, 1)`_`r sample(1000:100000, size=1)`@gmail.com <br>
<b>To:</b> provost@`r city_name`.co.uk <br>
<b>Cc:</b>
<b>Subject:</b> This `r sample(adj1, 1)` Pandemic

Dear Provost,

I am `r sample(emotion1, 1)` to hear about this new pandemic in `r city_name`. `r sample(sent1, 1)` 

I `r sample(wish1, 1)` that your office is going to do something about `r sample(state1, 1)` `r sample(time1, 1)`.

`r sample(clos1, 1, replace=TRUE)`<br>
`r sample(name1, 1)`

***

<b>From:</b> `r sample(email1, 1)`_`r sample(1000:100000, size=1)`@gmail.com <br>
<b>To:</b> provost@`r city_name`.co.uk <br>
<b>Cc:</b> city-council@`r city_name`.co.uk <br>
<b>Subject:</b> Pandemic Disaster for Businesses

Dear Provost,

This new pandemic in `r city_name` has the potential to `r sample(verb1, 1)` our businesses. I run a `r sample(business1, 1)` on the high street and `r sample(adj2, 1)` `r sample(conseq1, 1)` due to COVID. 

`r sample(sent2, 1)` 

I `r sample(wish1, 1)` that your office is going to do something about `r sample(state1, 1)` `r sample(time1, 1)`, keeping in mind the economic interests of businesses in our city and the fact that we cannot afford `r sample(conseq2, 1)`.<br>

`r sample(clos1, 1, replace=TRUE)`<br>
`r sample(name1, 1)` (`r sample(business2, 1)`, proprietor)

***

<b>From:</b> `r sample(email1, 1)`_`r sample(1000:100000, size=1)`@gmail.com <br>
<b>To:</b> provost@`r city_name`.co.uk <br>
<b>Cc:</b> city-council@`r city_name`.co.uk <br>
<b>Subject:</b> `r sample(subj1, 1)`

Dear Provost,

I `r sample(wish2, 1)` that you and your office are going to use this new pandemic as yet another excuse for government overreach into citizens' lives. `r sample(sent3, 1)` 

`r sample(sent4, 1)` 

`r sample(clos1, 1, replace=TRUE)`<br>
`r sample(name1, 1)` (a concerned voter)

***

<b>From:</b> `r sample(email1, 1)`_`r sample(1000:100000, size=1)`@gmail.com <br>
<b>To:</b> provost@`r city_name`.co.uk <br>
<b>Cc:</b> city-council@`r city_name`.co.uk <br>
<b>Subject:</b> 

Dear Provost,

I have just learned that my `r sample(rel1, 1)` has passed away due to the new pandemic in `r city_name`. `r sample(sent5, 1)` 

`r sample(sent5, 1)` 

`r sample(sent6, 1)` 

`r sample(clos1, 1, replace=TRUE)`<br>
`r sample(name1, 1)` 

***


As Provost of `r city_name`, you are of course familiar with the work of the [Standing Committee on Pandemic Preparedness](https://www.gov.scot/groups/standing-committee-on-pandemic-preparedness/). You are also familiar with:

* The [UK Pandemic Preparedness plan](https://www.gov.uk/government/publications/uk-pandemic-preparedness/uk-pandemic-preparedness)

* The latest [COVID-19 health protection guidance](https://publichealthscotland.scot/our-areas-of-work/conditions-and-diseases/covid-19/covid-19-health-protection-guidance/#section-1) released by Public Health Scotland

* [Tackling antimicrobial resistance 2019–2024: The UK’s five-year national action plan](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1070263/UK_AMR_5_year_national_action_plan.pdf)

* The [UK One Health Report - Joint report on antibiotic use and antibiotic resistance, 2013–2017 ](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/921039/Ted_Final_version__1318703-v45-One_Health_Report_2019_FINAL-accessible.pdf)

* [Communicating risk in public health emergencies: A WHO guideline for emergency risk communication (ERC) policy and practice](https://apps.who.int/iris/bitstream/handle/10665/259807/9789241550208-eng.pdf?sequence=2&isAllowed=y)



***

## Information Packet F2

You are a representative from Public Health Scotland, sent to `r city_name` to help with the <i>Neisseria</i> outbreak. 

Your briefing packet includes the following documents: 

* [Guidance for public health management of meningococcal disease in the UK](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/829326/PHE_meningo_disease_guideline.pdf)

* [Meningococcal ACWY vaccine surveillance and data - Public Health Scotland](https://publichealthscotland.scot/our-areas-of-work/immunisations/immunisations-by-vaccine/meningococcal-acwy-vaccine-men-acwy/surveillance-and-data/)

* [National enhanced surveillance of vaccination programmes targeting invasive meningococcal disease in England (UKHSA)](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/1124997/UKHSA-meningococcal-surveillance-december-2022.pdf)

* Alderson, Mark R et al. “Surveillance and control of meningococcal disease in the COVID-19 era: A Global Meningococcal Initiative review.” The Journal of infection vol. 84,3 (2022): 289-296. doi:10.1016/j.jinf.2021.11.016

* Muttalif, Abdul Razak et al. “Incidence and Prevention of Invasive Meningococcal Disease in Global Mass Gathering Events.” Infectious diseases and therapy vol. 8,4 (2019): 569-579. doi:10.1007/s40121-019-00262-9

***

## Information Packet F3

You are an epidemiologist working for Public Health Scotland, sent to `r city_name` to help with the <i>Neisseria</i> outbreak.

A team of scientists working together have in a PHS lab have isolated and cultured <i>Neisseria</i> (following standard procedures) from a number of patient samples taken during this outbreak; isolated DNA from these cultures; sequenced this DNA using an Illumina MiSeq platform; assembled the short paired-end reads; and compared these assemblies to the extant <i>Neisseria</i> sequences available in the NCBI databases. The results of these experiments are summarised in the table below. 

<table>
<table border="1">
  <tr>
    <th>Patient  </th>
    <th>NCBI accession of closest database match</th>
  </tr>
  <tr>
    <td>1</td>
    <td>GCA_003496325.1</td>
  </tr>
  <tr>
    <td>2</td>
    <td>GCA_003977735.1</td>
  </tr>
  <tr>
    <td>3</td>
    <td>GCA_003496325.1</td>
  </tr>
  <tr>
    <td>4</td>
    <td>GCA_003496325.1</td>
  </tr>
  <tr>
    <td>5</td>
    <td>GCA_003496325.1</td>
  </tr>
  <tr>
    <td>6</td>
    <td>GCA_003496325.1</td>
  </tr>
    <tr>
    <td>7</td>
    <td>GCA_003496325.1</td>
  </tr>
  <tr>
    <td>8</td>
    <td>GCA_003496325.1</td>
  </tr>
  <tr>
    <td>9</td>
    <td>GCA_003977745.1</td>
  </tr>
    <tr>
    <td>10</td>
    <td>GCA_003496325.1</td>
  </tr>
</table>  
<br><br>
Your briefing packet also includes the following documents: 

* [<i>Neisseria</i> spp. pubMLST](https://pubmlst.org/organisms/neisseria-spp)

* Schoen, Christoph et al. “Whole-genome comparison of disease and carriage strains provides insights into virulence evolution in <i>Neisseria meningitidis</i>.” Proceedings of the National Academy of Sciences of the United States of America vol. 105,9 (2008): 3473-8. doi:10.1073/pnas.0800151105

* Itsko, Mark et al. “Enhancing Meningococcal Genomic Surveillance in the Meningitis Belt Using High-Resolution Culture-Free Whole-Genome Sequencing.” The Journal of infectious diseases vol. 226,4 (2022): 729-737. doi:10.1093/infdis/jiac104

* de Souza Santos, Debora Ribeiro et al. “High-Resolution Melting (HRM) for rapid MLST analysis of <i>Neisseria meningitidis</i>.” Journal of microbiological methods vol. 200 (2022): 106557. doi:10.1016/j.mimet.2022.106557

***

## Information Packet F4

You are the director of `r city_name`'s main hospital, the `r hospital_name`, which has 550 beds across 9 different wards and 10 operating theatres. 


```{r hospital, echo=FALSE, fig.cap="The Royal Jubilee hospital in Glenmarigg. Image credit: [DALL-E"}
knitr::include_graphics(rep("images/Queens-College.png"))
```

The annual operating budget for financial year 2021-2022 was £1.5 million, and average expenditures are shown by category in the figure below. 

```{r A5, fig.cap="Hospital expenditures by category for financial year 2021-2022 (Source: NHS Scotland)", echo=FALSE}

expenses <- data.frame(
  Category=c("Staff costs", "Healthcare expenditures (drugs, supplies, etc.)", "Other supplies", "Other running costs (procurement, IT, HR, etc.)"),
  value=c(sample(25:35, size=1), sample(18:27, size=1), sample(4:10, size=1), sample(5:11, size=1))
)

ggplot(expenses, aes(x="", y=value, fill=Category)) +
  geom_bar(stat="identity", width=1, color="white") +
  coord_polar("y", start=0) +
  theme_void() 

```

The `r hospital_name` has units specialising in coronary care; maternity care; dermatology; gastroenterology; an ear, nose, and throat clinic; an eye clinic; and an orthopedic unit.

There are currently 25 ICU beds (with ventilators) available, an increase from the 14 ICU beds in the `r hospital_name` in November 2019. Average ICU bed occupancy before and during the COVID-19 pandemic is in the figure below. 


```{r A6, fig.cap="ICU bed occupancy for the Glenmarigg Royal Jubilee hospital (Source: NHS Scotland)", echo=FALSE}

ICU <- c(sample(10:15, size=16, replace=TRUE), sample(23:25, size=4, replace=TRUE), sample(17:20, size=4, replace=TRUE), sample(22:25, size=4, replace=TRUE), sample(15:20, size=5, replace=TRUE), sample(22:25, size=3, replace=TRUE), sample(15:20, size=4, replace=TRUE), sample(22:25, size=4, replace=TRUE), sample(17:21, size=4, replace=TRUE))
ICUdates <- c("1/2019", "2/2019", "3/2019", "4/2019", "5/2019", "6/2019", "7/2019", "8/2019", "9/2019", "10/2019", "11/2019", "12/2019", "1/2020", "2/2020", "3/2020", "4/2020", "5/2020", "6/2020", "7/2020", "8/2020", "9/2020", "10/2020", "11/2020", "12/2020", "1/2021", "2/2021", "3/2021", "4/2021", "5/2021", "6/2021", "7/2021", "8/2021", "9/2021", "10/2021", "11/2021", "12/2021","1/2022", "2/2022", "3/2022", "4/2022", "5/2022", "6/2022", "7/2022", "8/2022", "9/2022", "10/2022", "11/2022", "12/2022")

ICUdates <- factor(ICUdates, levels = ICUdates)

ICUstats <- data.frame(ICU, ICUdates)
ggplot(data = ICUstats, aes(x=ICUdates, y=ICU, group = 1)) + 
  geom_point() +
  geom_line() +
  labs(y = "Average Royal Jubilee ICU bed occupancy/month", x = "Month") +
  scale_y_continuous(limits=c(0, 25)) + 
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) + 
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
```


There are approximately 1.3m admissions to the `r hospital_name` hospital annually, the majority of these being to the emergency (A&E) department.

```{r A7, fig.cap="Admissions to the Glenmarigg Royal Jubilee hospital by category (Source: NHS Scotland)", echo=FALSE}

admissions <- data.frame(
  Category=c("Elective Inpatient", "A&E", "Day case"),
  value=c(sample(15:25, size=1), sample(50:70, size=1), sample(20:25, size=1))
)

ggplot(admissions, aes(x="", y=value, fill=Category)) +
  geom_bar(stat="identity", width=1, color="white") +
  coord_polar("y", start=0) +
  theme_void() 

```


A&E waiting times have been called "disastrously high" in recent months, both by the press and by tthe hospital ombudsman.

```{r A8, fig.cap="ICU waiting times for the Glenmarigg Royal Jubilee hospital (Source: NHS Scotland)", echo=FALSE}

WaitTimes <- c(sample(1:2, size=16, replace=TRUE), sample(1:2, size=4, replace=TRUE), sample(2:4, size=4, replace=TRUE), sample(2:5, size=4, replace=TRUE), sample(1:5, size=5, replace=TRUE), sample(2:5, size=3, replace=TRUE), sample(3:5, size=4, replace=TRUE), sample(2:5, size=4, replace=TRUE), sample(5:6, size=4, replace=TRUE))
AEdates <- c("1/2019", "2/2019", "3/2019", "4/2019", "5/2019", "6/2019", "7/2019", "8/2019", "9/2019", "10/2019", "11/2019", "12/2019", "1/2020", "2/2020", "3/2020", "4/2020", "5/2020", "6/2020", "7/2020", "8/2020", "9/2020", "10/2020", "11/2020", "12/2020", "1/2021", "2/2021", "3/2021", "4/2021", "5/2021", "6/2021", "7/2021", "8/2021", "9/2021", "10/2021", "11/2021", "12/2021","1/2022", "2/2022", "3/2022", "4/2022", "5/2022", "6/2022", "7/2022", "8/2022", "9/2022", "10/2022", "11/2022", "12/2022")

AEdates <- factor(AEdates, levels = AEdates)

AEwaits <- data.frame(WaitTimes, AEdates)
ggplot(data = AEwaits, aes(x=AEdates, y=WaitTimes, group = 1)) + 
  geom_point() +
  geom_line() +
  labs(y = "Percentage of A&E patients with a wait time > 4 hours", x = "Month") +
  scale_y_continuous(limits=c(0, 15)) + 
  theme(axis.text.x = element_text(angle = 90, vjust = 0.5, hjust=1)) + 
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())
```


The `r hospital_name` has been set a goal of 25% reduction in sepsis mortality (compared to past years)and 50% reduction in the nosocomial transmission of superbugs such as methicillin-resistant <i>Staphylococcus aureus</i> (MRSA), <i>Clostridiodes difficile</i> (C. diff), and <i>Candida auris</i> (C. auris). 

```{r A9, fig.cap="Key Performance Indicators (KPIs) related to infectious diseases for the Glenmarigg Royal Jubilee hospital (Source: NHS Scotland)", echo=FALSE}

hosKPIs <- data.frame(
  KPI=c("Reduction in MRSA cases", "Reduction in C diff cases", "Reduction in sepsis mortality", "Reduction in C auris cases"),
  percent=c(sample(55:65, size=1), sample(30:70, size=1), sample(5:15, size=1), sample(15:40, size=1))
)

ggplot(hosKPIs, aes(x = KPI, y = percent)) +
  geom_col() +
  coord_flip() +
  scale_y_continuous(limits=c(0, 100)) +
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())

```

There are currently `r sample(143:180, size=1)` patients in the `r hospital_name` with confirmed or suspected meningococcal disease, with `r sample(15:17, size=1)` of these patients currently in the ICU. 

The hospital follows the guidelines set out in the [National Infection Prevention and Control Manual](https://www.nipcm.hps.scot.nhs.uk/).

As a hospital director, you are familiar with the literature surrounding hospital pandemic preparedness, and regularly read papers such as:

* Mer, Mervyn et al. “Critical Care Pandemic Preparation: Considerations and Lessons Learned from COVID-19.” Critical care clinics vol. 38,4 (2022): 761-774. 

* Tacconelli, Evelina et al. “Challenges of data sharing in European Covid-19 projects: A learning opportunity for advancing pandemic preparedness and response.” The Lancet regional health. Europe vol. 21 (2022): 100467. 

* Adelaja, I., Sayma, M., Walton, H., McLachlan, G., de Boisanger, J., Bartlett-Pestell, S., Roche, E., Gandhi, V., Wilson, G. J., Brookes, Z., Yeen Fung, C., Macfarlane, H., Navaratnam, A., James, C., Scolding, P., & Sara, H. (2020). A comprehensive hospital agile preparedness (CHAPs) tool for pandemic preparedness, based on the COVID-19 experience. Future healthcare journal, 7(2), 165–168. 

***

## Information Packet F5

You are a civil servant working in `r city_name`, working closely with the provost, city council and various agencies including the NHS, the UK Health Security Agency (UKHSA), and the Scottish Environment Protection Agency (SEPA).  

Some of the key `r city_name` facts and figures at a glance are summarized in the table below.

<table>
<table border="1">
  <tr>
    <th>Community Amenities</th>
    <th>Details</th>
  </tr>
  <tr>
    <td>Schools</td>
    <td>`r sample(2:8, size=1)` primary schools, `r sample(2:5, size=1)` secondary schools, 2 universities</td>
  </tr>
  <tr>
    <td>Care Homes</td>
    <td>`r sample(1:5, size=1)`, each with ~`r sample(c(30, 40, 45, 50), size=1)` bed capacity</td>
  </tr>
  <tr>
    <td>Restaurants and Cafes</td>
    <td>`r sample(50:150, size=1)`</td>
  </tr>
    <tr>
    <td>Parks and Playgrounds</td>
    <td>`r sample(1:15, size=1)`</td>
  </tr>
  <tr>
  <th>Economic Indicators</th>
  <th>Details</th>
  </tr>
  <tr>
  <td>GDP/capita</td>
  <td>£`r sample(36000:50000, size=1)`</td>
  </tr>
  <tr>
  <td>Unemployment Rate</td>
  <td>`r sample(3:8, size=1)`%</td>
  </tr>
  <tr>
  <th>Traffic and Transport</th>
  <th>Details</th>
  </tr>
  <tr>
  <td>Traffic fatalities (average/month)</td>
  <td>`r sample(5:20, size=1)`</td>
  </tr>
</table>  
<br><br>


Your briefing packet on <i>Neisseria</i> includes the following information.

* [Meningococcal Disease Risk Factors](https://www.cdc.gov/meningococcal/about/risk-factors.html)

* [Meningitis and septicaemia: prevention and management in higher education institutions](https://www.gov.uk/government/publications/meningitis-and-septicaemia-prevention-and-management-in-higher-education-institutions)

* Sulis, Giorgia et al. “A comparison of national vaccination policies to prevent serogroup B meningococcal disease.” Vaccine vol. 40,26 (2022): 3647-3654.

* Taha, Muhamed-Kheir et al. “Equity in vaccination policies to overcome social deprivation as a risk factor for invasive meningococcal disease.” Expert review of vaccines vol. 21,5 (2022): 659-674. doi:10.1080/14760584.2022.2052048

* Martinón-Torres, Federico et al. “Evolving strategies for meningococcal vaccination in Europe: Overview and key determinants for current and future considerations.” Pathogens and global health vol. 116,2 (2022): 85-98. doi:10.1080/20477724.2021.1972663

***

## Information Packet F6

You are a microbiologist working in the microbiology department at the Greater `r city_name` Clinical Laboratory. Your laboratory is equipped to handle a range of culture samples (including anaerobic and microaerobic bacteria, as well as viruses), and you routinely process`r sample(1500:2000, size=1)` samples monthly. 

You are familiar with the culture requirements for growth of <i>Neisseria</i> spp. in culture, and the range of [UK Standards for Microbiology Investigations (UK SMI) for Screening for <i>Neisseria</i>](https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/343978/B_51i2.pdf).

```{r Neisseria-plate, echo=FALSE, fig.cap="Neisseria meningiditis colonies on a Blood Agar plate. Image credit: [CDC](https://www.cdc.gov/meningitis/lab-manual/chpt07-id-characterization-nm.html)"}
knitr::include_graphics(rep("images/Neisseria-BloodAgar.gif"))
```

You are also familiar with the literature surrounding <i>Neisseria meningitidis</i> identification, and often read papers such as:

* [Identification and Characterization of <i>Neisseria meningitidis</i> (CDC)](https://www.cdc.gov/meningitis/lab-manual/chpt07-id-characterization-nm.html)

* Morsli, Madjid et al. “Real-time metagenomics-based diagnosis of community-acquired meningitis: A prospective series, southern France.” EBioMedicine vol. 84 (2022): 104247.

* Sharma, Nupur et al. “Clinical use of multiplex-PCR for the diagnosis of acute bacterial meningitis.” Journal of family medicine and primary care vol. 11,2 (2022): 593-598.



***

## Information Packet F7

You are a public communications expert, often employed by the `r city_name` city council to manage the PR response to different initiatives or crises. 

As a public communications expert, you are familiar with the literature surrounding science communication in a pandemic, including papers such as: 

* Matta, G. Science communication as a preventative tool in the COVID19 pandemic. Humanit Soc Sci Commun 7, 159 (2020).

* Abdool Karim, Salim S. “Public understanding of science: Communicating in the midst of a pandemic.” Public understanding of science (Bristol, England) vol. 31,3 (2022): 282-287.

* Royan, Regina et al. “Use of Twitter Amplifiers by Medical Professionals to Combat Misinformation During the COVID-19 Pandemic.” Journal of medical Internet research vol. 24,7 e38324. 22 Jul. 2022, doi:10.2196/38324

* Tait, Margaret E et al. “Serving the public? A content analysis of COVID-19 public service announcements airing from March - December of 2020 in the U.S.” Preventive medicine reports vol. 29 (2022): 101971. 

You have assembled the following information/resources for this meeting:

* [WHO Initiative: Defeating Meningitis by 2030](https://www.who.int/initiatives/defeating-meningitis-by-2030)

* [Meningitis Now Resources](https://www.meningitisnow.org/how-we-help/resources/)

* [Meningitis Research Foundation: Help and Support Resources](https://www.meningitis.org/get-support/help-and-support-resources)

* Webb, Adam et al. “Cross-Sectional Study of University Students' Attitudes to 'On Campus' Delivery of COVID-19, MenACWY and MMR Vaccines and Future-Proofing Vaccine Roll-Out Strategies.” Vaccines vol. 10,8 1287. 10 Aug. 2022, doi:10.3390/vaccines10081287

***

## Information Packet F8

You are one of the doctors at the largest surgery in `r city_name`. In the past fortnight, `r sample(50:100, size=1)` of your patients have recently presented to the surgery with symptoms consistent with meningiditis. You have therefore recently been familiarising yourself with the relevant literature:

* [Meningococcal Disease: Clinical Info (CDC)](https://www.cdc.gov/meningococcal/clinical-info.html)

* [BMJ Best Practice - Bacterial Meningitis in Adults](https://bestpractice.bmj.com/topics/en-gb/3000104)

* [Meningitis (bacterial) and meningococcal septicaemia in under 16s: recognition, diagnosis and management (NICE)](https://www.nice.org.uk/guidance/cg102)

* [Meningococcal Disease: Infection Control in Healthcare Personnel: Epidemiology and Control of Selected Infections Transmitted Among Healthcare Personnel and Patients](https://www.cdc.gov/infectioncontrol/guidelines/healthcare-personnel/selected-infections/meningococcal-disease.html)

* Hasbun, Rodrigo. “Progress and Challenges in Bacterial Meningitis: A Review.” JAMA vol. 328,21 (2022): 2147-2154. doi:10.1001/jama.2022.20521

* McNamara, Lucy A et al. “Mass chemoprophylaxis for control of outbreaks of meningococcal disease.” The Lancet. Infectious diseases vol. 18,9 (2018): e272-e281.

* Davis, L C et al. “Meningococcal disease in a backpackers hostel in Scotland: a risk assessment for prophylaxis.” Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin vol. 14,31 19291. 6 Aug. 2009, doi:10.2807/ese.14.31.19291-en