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Issue neherlab#687, cotninued: Improve styling of pages, optimize readability on /faq page
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samanthahamilton committed Aug 3, 2020
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85 changes: 43 additions & 42 deletions src/assets/text/faq.mdx
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Expand Up @@ -6,9 +6,9 @@ import youtubeTutorialThumbnail from '../img/youtube-tutorial-thumbnail.jpg'

<Container>

**Q:** How to use this tool? Is there a tutorial?
**Q:** How do I use this tool? Is there a tutorial?

**A:** _Tutorial video is available on YouTube:_
**A:** _Our tutorial video is available on YouTube:_

<Row>
<Col className="d-flex">
Expand All @@ -17,61 +17,62 @@ import youtubeTutorialThumbnail from '../img/youtube-tutorial-thumbnail.jpg'
</LinkExternal>
</Col>
</Row>

---

**Q:** How do I refer to the tool in publications? Is there a paper?

**A:** _We have posted a [preprint](https://www.medrxiv.org/content/10.1101/2020.05.05.20091363v2) describing covid19-scenarios.org
on medrxiv. Please use this as a reference until our work appears in a journal.
[doi: 10.1101/2020.05.05.20091363](https://doi.org/10.1101/2020.05.05.20091363 )_
**A:** _We have posted a preprint describing covid19-scenarios.org on medRxiv. Please use this as a reference until our
work appears in a journal. [doi: 10.1101/2020.05.05.20091363](https://doi.org/10.1101/2020.05.05.20091363 )_

---

**Q:** Why does the outbreak grow more slowly when I increase the infectious period?

**A:** _The number of secondary cases a particular case causes is specified by R0. If you increase the infectious
period, the same number of infections happen over a longer period. Hence the outbreak grows more slowly._
**A:** _The number of secondary cases resulting from a particular case is specified by $R_0$. If you increase the infectious
period, the same number of infections occur, but over a longer time period. Hence the outbreak grows more slowly._

---

**Q:** Why is the number of severe cases lower than the number of critical cases?

**A:** _COVID-19 cases in critical condition need intensive care for a long time. Our model assumes that they spend on
average 14 days in the ICU. The severely ill (our proxy for those in need of a regular hospital bed) either deteriorate
fast or recover (default in our model is four days). Hence at any given point in time, the number of critically ill
people might exceed the number of severely ill._
**A:** _Critical condition COVID-19 cases need intensive care for a long time. Our model assumes that they spend an
average of 14 days in the ICU. Severely ill is our proxy for those in need of a regular hospital bed. These individuals will either deteriorate
rapidly or recover (default recovery time in our model is 4 days). Therefore, at any given point in time, the number of critically ill
people can exceed the number of severely ill._

---

**Q:** Is the model fit to observations?

**A:** _Yes, provided we have a good source of COVID-19 cases, we fit a few model parameters to observations.
Specifically, we estimate R0, the initial size and date of the epidemic, and the case underreporting fraction. For case
severity information, we utilize estimate from case outcome data from China._ Currently mitigation efforts, both the
timing and the efficacy are _not_ estimated from the data. We are actively looking for user-provided dates for
mitigation efforts for your regions of interest.
**A:** _Yes, provided we have a good source of COVID-19 cases, we fit several model parameters to observations.
Specifically, we estimate $R_0$, the initial size and date of the epidemic, and the case underreporting fraction. For case
severity information we utilize an estimate from case outcome data from China._

Note: Currently mitigation efforts, both the timing and the efficacy, are _not_ estimated from the data.
We are actively looking for user-provided dates of mitigation efforts for your region(s) of interest.

---

**Q:** My country/region/town is missing!
**Q:** My town/region/country is missing!

**A:** _If you have suggestions on additional regions that should be covered, head over to
[our data directory](https://github.com/neherlab/covid19_scenarios/tree/master/data) and make a pull request!_
**A:** _If you have suggestions on additional regions that should be covered, head over to our
[GitHub data directory](https://github.com/neherlab/covid19_scenarios/tree/master/data) and make a pull request!_

---

**Q:** What is ICU overflow?
**Q:** What is "ICU overflow"?

**A:** _In places that have seen severe COVID-19 outbreak, the capacity of intensive care facilities is quickly
exhausted. Patients that need ventilation but can't get ventilation due to shortage will die faster. "ICU overflow" is
our label for critically ill patients that should be ventilated but are not since no ventilators are available. These
patients will die faster. The degree to which they die faster is specified by the `Severity of ICU overflow` parameter._
**A:** _In places that have seen a severe COVID-19 outbreak, the capacity of intensive care facilities is quickly
exhausted. Due to the resulting resource shortage, patients that need ventilation cannot get access. "ICU overflow" is
our label for critically ill patients that should be ventilated, but are NOT, since no ventilators are available. These
patients will die faster; the degree to which is specified by the `Severity of ICU overflow` parameter._

---

**Q:** Wouldn't it be a good idea to model isolation of specific age-groups?
**Q:** Wouldn't it be a good idea to model the isolation of specific age-groups?

**A:** _Yes! This is indeed possible on covid-scenarios. Expand the card
**A:** _Yes! This is indeed possible on [covid-scenarios](https://covid19-scenarios.org/). Expand the card
`Severity assumptions and age-specific isolation`. The last column allows you to specify to what extent individual age
groups are isolated from the rest of the population._

Expand All @@ -81,51 +82,51 @@ groups are isolated from the rest of the population._

**A:** _You are probably referring to the
[March 16 report by Neil Ferguson et al](https://www.imperial.ac.uk/media/imperial-college/medicine/sph/ide/gida-fellowships/Imperial-College-COVID19-NPI-modelling-16-03-2020.pdf).
Like us, Ferguson et al model the effect of interventions on the spread of COVID-19 using a computational model. Their
Like us, Ferguson et al. use a computational model to investigate the effect of interventions on the spread of COVID-19. Their
model is individual based, meaning their program represents a large number of individuals among whom the virus is
spreading. Our model breaks the population into age-groups and different categories corresponding to susceptible,
infected, dead, recovered, etc. This allows for faster simulations, but loses some realism. The faster simulation allows
exploration of parameters._
spreading. Our model breaks the population into age-groups and different categories corresponding to those susceptible,
infected, dead, recovered, etc. While this may lose some realism, our model type allows for faster simulations and
exploration of various parameters._

---

**Q:** What do the parameter ranges correspond to?

**A:** _Parameter ranges allow the user to specify the distribution of possible values. We assume a uniform prior, i.e.
any value within the range has an equal probability of being chosen. The model is then run from a Monte Carlo sampling from
all specified parameter ranges for user tunable number of samples. The median trajectory, as well as the 20% and 80% percentiles
**A:** _Parameter ranges allow the user to specify the distribution of possible values. We assume a uniform prior, i.e.,
any value within the range has an equal probability of being chosen. The model is then run with a Monte Carlo sampling from
all specified parameter ranges for user-specified number of samples. The median trajectory, as well as the 20th and 80th percentiles,
are displayed as the shaded uncertainty region._

---

**Q:** Why do the curves sometimes have strange kinks?

**A:** _The curves show the median of a number simulations sampled from the parameter ranges. If the simulations
corresponding to different parameter combinations intersect, the curve representing the median can change
corresponding to different parameter combinations intersect, the curve representing the median can change,
resulting in a kink._

---

**Q:** What is a good number of simulations to run?

**A:** _We chose 15 as the default as this is a good balance between sufficient sampling and maintaining interactivity.
Once you find a set of parameters that you find reasonable, we suggest to increase the number to more accurately capture
**A:** _We chose 15 as the default number of simulations to run. This is a good balance between sufficient sampling and maintaining interactivity.
Once you have discovered a set of parameters that you find reasonable, we suggest increasing the number to more accurately capture
the statistics._

---

**Q:** Can I run a simulation with no uncertainty?

**A:** _If you set the lower and upper bounds of each parameter to the same value, you'll only get one curve
and no uncertainty bands. In this case the number of simulation runs is ignored._
**A:** _If you set the lower and upper bounds of each parameter to the same value, your result will include only get one curve
and no uncertainty bands. Note that in this case the number of simulation runs is ignored._

---

**Q:** How to interpret the figures reported under "Proportions"? Is a fatal case also counted as critical or severe case? Is a critical case also counted as severe case?
**Q:** How do I interpret the figures reported under "Proportions"? Is a fatal case also counted as critical or severe case? Is a critical case also counted as severe case?

**A:** _A: These numbers sum to 100%. The number reported as "critical" is the fraction of infected people that fall critically ill but didn't die.
Similarly, the reported fraction of "severe" cases is the fraction of cases that get severely ill but don't need critical care.
In summary, these numbers report the most serious outcome for each case._
**A:** _These numbers sum to 100%. The number reported as "critical" is the fraction of infected people that fall critically ill but did not die.
Similarly, the reported fraction of "severe" cases is the proportion of cases that were severely ill but did not need critical care.
In essence, these numbers report the most serious outcome for each case._


</Container>

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