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[WSG21] Daily Study Group: Building and Applying Epidemic Models

A new study group for Building and Applying Epidemic Models with the Wolfram Language begins Monday, May 10, 2021!

Making progress in an online course can be daunting when you have to study all alone. Join a cohort of fellow Wolfram Language users for a two-week study group in which you will start in week one with the basics of implementing compartment-based epidemiological models in the Wolfram Language. In the second week, you will cover multi-group models–taking into account vital demographics (i.e. birth, death) and age groups–in addition to introducing control measures and ending with stochastic models.

Sign up here: https://wolfr.am/UZfPoLAq

55 Replies

I just register up for this course!
Where can I download the course series notebook file?

POSTED BY: Tsai Ming-Chou
Posted 4 years ago

Dear Dr. Robert, Greetings and thanks to you for every help and recommendation you did. I wonder regarding the function "DiseaseFreeEquilibirium" it seems not available and the font remains in blue. Once I used the next-generation method function to evaluate the controlled reproduction number for my vaccinated model will run forever without reaching any output! So how to define the equilibrium point in our calculation using your wonderful packages? I followed the same as you did in your session for "Host-Vector Models Treatment and Vaccination Models" Thanks and regards

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POSTED BY: Manal Almuzini
Posted 4 years ago

Unfortunately, same error, I did to group the infectious compartments together! is there any other error?

POSTED BY: Manal Almuzini
Posted 4 years ago

Hi Mr. Jeremy, Thanks for your feedback. Really I did via Dr. Robert's package, but it seems something went wrong or I missed some critical point if you could guide me? This is the screenshot. Maybe because I used the vital demographic as well? Regards.

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POSTED BY: Manal Almuzini
Posted 4 years ago
POSTED BY: Manal Almuzini

The endemic equilibria can be found with Solve, the way you have been trying. I may just take a long time to get a fully symbolic solution. Unless you want to prove that an endemic equilibrium is unstable when R0 < 1, you generally don't need to determine it symbolically.

For data fitting, it's easier to do things numerically, and an endemic equilibrium can be included in the fitting data.

Regarding the asymptomatic compartment A, if counts of asymptomatic people are not available yo just don't include that compartment in the fitting data. Assuming 0 and would be a mistake.

When using standard incidence for the force of infection, the death compartment(s) are excluded from the denominator, just as you suggest. You can do as N[t]-D[t] or as S[t]+E[t]+A[t]+I[t]+R[t]+V[t].

I'll have to poke around for a data source for UAE cases and deaths.

POSTED BY: Robert Nachbar
Posted 4 years ago
POSTED BY: Manal Almuzini
POSTED BY: Robert Nachbar
Posted 4 years ago
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POSTED BY: Manal Almuzini
Posted 4 years ago

Thanks a lot for your clarifications, recommendations, and prompt response. Regards

POSTED BY: Updating Name
POSTED BY: Robert Nachbar
Posted 4 years ago
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POSTED BY: Manal Almuzini
POSTED BY: Robert Nachbar
Posted 4 years ago

Dear Dr. Nachbar, Greetings. Thanks for your continuous help and support, for my model SVEAIRS including vital demographic and vaccination, I wonder regarding the treatment model data give an output percentage as shown? moreover, the ngm command gives me an error as well? any comments or suggestions? Thanks again and regards

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POSTED BY: Manal Almuzini
POSTED BY: Robert Nachbar
Posted 4 years ago

Unfortunately, same error, I did to group the infectious compartments together! is there any other error?

Attachment

Attachments:
POSTED BY: Manal Almuzini
Posted 4 years ago
POSTED BY: Manal Almuzini
POSTED BY: Robert Nachbar
Posted 4 years ago

Really many thanks. It works. But unfortunately, once I tried to include the DynamicTransmissionModel to include Birth and death rates I faced the same issue! I tried to solve but couldn't? I avoided the subscripts to avoid coding error. THANKS here is my code

POSTED BY: Manal Almuzini
POSTED BY: Robert Nachbar
Posted 4 years ago
POSTED BY: Manal Almuzini

The thread is fast and works fine with me. Feel free to use the feature that suits you best.

POSTED BY: Ahmed Elbanna
Posted 4 years ago

Sorry, I thought that is how I had attached my two .nb that are cluttering the forum

POSTED BY: Peter Aptaker

Yes Peter, you can attach a notebook file without preview using the button "Add a file to this post" located at the end of the editor as shown in the below image. You can also publish a notebook in cloud and provide the link. enter image description here

POSTED BY: Ahmed Elbanna
Posted 4 years ago

Is there a way I can default any .nb attachments to "not preview" to avoid cluttering the Forum? Or should they either be shorter, not sent and sent elsewhere?

POSTED BY: Peter Aptaker
POSTED BY: Robert Nachbar
Posted 4 years ago
POSTED BY: Doug Beveridge
Posted 4 years ago
POSTED BY: Peter Aptaker
Posted 4 years ago
POSTED BY: Peter Aptaker
POSTED BY: Robert Nachbar
POSTED BY: Robert Nachbar
POSTED BY: Robert Nachbar
Posted 4 years ago

Hello All!

Sorry for putting this up here so late, but I noticed an error I've been getting with the first notebook of this series. I don't see a population key for AdmistrativeRegion so perhaps that is why i'm getting the error so these lines of code don't render?

Error I'm Receiving

POSTED BY: Hector Naranjo
Posted 4 years ago

It would be excellent if you (Robert N) could comment on this some time (it relates to he previous post)

POSTED BY: Peter Aptaker
Posted 4 years ago

If I want the absolute vaccination rate to be controlled do I really need a "negative sink". see attached .nb

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POSTED BY: Peter Aptaker
Posted 4 years ago

Can you give any analytical insight into "infections/lives saved" as function of vaccine rollout rate? Clearly it is easy, if vaccination is "instant" and I have had success assuming vaccine rollout is far faster than new infections. I appreciate that "lives" is harder that "cases", with age stratification on both vaccine rollout and mortality but that is not my question.

POSTED BY: Peter Aptaker
Posted 4 years ago

Has the Stochastic Models video been released ?

POSTED BY: Doug Beveridge
Posted 4 years ago

In the DynamicTransmissionModel function, if the option AgeStratification is not enabled, the ForceOfInfection is effectively the probability of one of the contacts made by the suseptibles being with one individual in an infective compartment; if the AgeStratification is enabled, the ForceOfInfection is effectively the multiplication of that probability and the contact rates. Why does this inconsistence exist?

POSTED BY: Feng Xu
Posted 4 years ago
POSTED BY: oliver frankel

The series materials are provided daily in the invitation link you get to join the session. You will get them there, but for now, if you have registered here is the link where you can get notebooks. Files for the series

Hopefully, I am not doing something wrong by sharing this.

POSTED BY: Ravi Kiran
Posted 4 years ago

Post registration (now done 3 times) I land here: https://www.bigmarker.com/series/daily-study-group-building-applying-epidemic-models/series_details but I see no NB links.

POSTED BY: oliver frankel

Register here

Then you should be able access the the materials.

POSTED BY: Robert Nachbar
Posted 4 years ago

Where are the study notebooks, please? I have joined very late....

POSTED BY: oliver frankel

NDSolve and ParametricNDSolve both return lists of Rules. I find it more convenient to work with those lists of Rules than just a list of their Values (right hand sides) as is done in your code. This way I work directly with the variables I need rather than some part of a list. (In general I try to avoid using Part.)

I also find it easier to solve for the variables vi rather than vi[t].

I made a couple changes to your code. In the first cell I used

seirCompartments = {\[ScriptCapitalS], \[ScriptCapitalE], \
\[ScriptCapitalI], \[ScriptCapitalR]};

and in the second cell I used

Plot[{\[ScriptCapitalS][\[Beta], \[Gamma], \[Sigma]][
     t], \[ScriptCapitalR][\[Beta], \[Gamma], \[Sigma]][t]} /. 
   seirSolutions // Evaluate, {t, 0, tmax}, 
 PlotRange -> {{0, tmax}, {0, ymax}}]
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POSTED BY: Robert Nachbar

Thank you so much, Rohit. This works if they are in order right. can I plot if they are not in order, say S and R.

Edit: Okay I got this from wolfram documentation on Part if anyone needs it here it is

POSTED BY: Ravi Kiran
Posted 4 years ago
POSTED BY: Rohit Namjoshi
POSTED BY: Ravi Kiran

Thank you.

POSTED BY: Bernardine Wong
Posted 4 years ago

Thank you. It worked well. If I may trouble you again: I did following your instructions for the ResourceFunction["COVID19EpidemicData"] found in WSG14_Session1.nb but got an unexpected result (as shown in the attachment). What did do wrong?

Attachment

POSTED BY: Bernardine Wong
Posted 4 years ago

I used

Keys[c19Data ][[1]]

c19Data [[All,{"AdministrativeDivision","TotalVaccineDosesAllocated"}]]
POSTED BY: Doug Beveridge

Related to the question asked, I would like to know the following: From c19Data = ResourceFunction["JHUCOVID19VaccineData"][] how do I determine what the keys are, and how do I extract a set of values, for example the time series corresponding to TotalVaccineDosesAllocated?

POSTED BY: Bernardine Wong
Posted 4 years ago

OK , it seems the menu

Evaluation \Dynamic Updating Enabled

must be enabled (have a tick )

then it loads

POSTED BY: Doug Beveridge
Posted 4 years ago
POSTED BY: Doug Beveridge
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