Re: [stem-dev] stem-dev Digest, Vol 135, Issue 8

["James Kaufman" <jhkauf@xxxxxxxxxx>]

Hi Frederico,

After you launch
STEM for the first time a folder called "workspace" is created.
On mac you have to "view package contents" on the stem app to
see it.
Navigate to workspace,
 your project is inside it. Inside the Project folder is the folder
"Recorded Simulations". You can create a subfolder (eg called
reference) and drop your incidence and population files there. 

When you relaunch
STEM you then need to go to the project explorer, click on your project,
right click, and chose "refresh". The Eclipse project explorer
will not synch with changes you made to the file system until you do that
refresh step.

you have to create
the reference incidence file. The easiest way to see precisely how it should
be formatted is to create a logger and log your models predicted incidence.
The file should be formatted and named just like that one.

Best Regards,
Jamie






From:
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Date:
       07/15/2020
09:01 AM
Subject:
       [EXTERNAL]
stem-dev Digest, Vol 135, Issue 8
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Today's Topics:

   1. Re: stem-dev Digest, Vol 135, Issue 6 (Frederico Mestre)


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Message: 1
Date: Wed, 15 Jul 2020 10:14:24 +0100
From: Frederico Mestre <fmestre@xxxxxxxxx>
To: STEM developer mailing list <stem-dev@xxxxxxxxxxx>
Subject: Re: [stem-dev] stem-dev Digest, Vol 135, Issue 6
Message-ID:
                
<CAASDe-5BPqkj_fuA=yMPOviLbnjVdPj5og94N5+8djTJah940g@xxxxxxxxxxxxxx>
Content-Type: text/plain; charset="utf-8"

Thanks.

How are the files uploaded to STEM (e.g. the indicence csv) ? And what
about formatting the files?

In the website you sent me you mention that:

"2. Reference data folder. This is the directory containing the reference
data. The directory must contain the same files that STEM generates in
its
log output folders, e.g. an I_2.csv, Incidence_2.csv, S_2.csv etc. The
current error function only requires the Incidence file. If the reference
files are located in a folder inside the current project, the location
is
specified in a platform neutral manner and the project and associated
automatic experiment can be shared with others."

How are the incidence files generated, forated and uploaded?

Sorry for all the questions...

thanks,
Frederico
?

James Kaufman <jhkauf@xxxxxxxxxx> escreveu no dia segunda, 13/07/2020
?(s)
17:08:

> Frederico,
>
> STEM provides a Nelder-Meade simplex algorithm which does precisely
that.
> https://wiki.eclipse.org/Running_an_Automated_Experiment
>
>
> There is also and example here....
>
> https://wiki.eclipse.org/2019_novel_Corona_Virus_Model#.28new.29_Advanced_SACIR.28S.29_model_capturing_Asymptomatic_Transmission
>
>
>
> From:        stem-dev-request@xxxxxxxxxxx
> To:        stem-dev@xxxxxxxxxxx
> Date:        07/13/2020 09:00 AM
> Subject:        [EXTERNAL] stem-dev Digest, Vol
135, Issue 6
> Sent by:        stem-dev-bounces@xxxxxxxxxxx
> ------------------------------
>
>
>
> Send stem-dev mailing list submissions to
>                 stem-dev@xxxxxxxxxxx
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> To subscribe or unsubscribe via the World Wide Web, visit
>                 https://www.eclipse.org/mailman/listinfo/stem-dev
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>                 stem-dev-request@xxxxxxxxxxx
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> Today's Topics:
>
>   1. Parameter estimation (Frederico Mestre)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 13 Jul 2020 11:20:02 +0100
> From: Frederico Mestre <fmestre@xxxxxxxxx>
> To: STEM developer mailing list <stem-dev@xxxxxxxxxxx>
> Subject: [stem-dev] Parameter estimation
> Message-ID:
>                 <CAASDe-6=+Z1WO7=
> 7-NNL687RY8eW082mhOjHMU-SqMDUvimEow@xxxxxxxxxxxxxx>
> Content-Type: text/plain; charset="utf-8"
>
> Hello,
>
> Quick question: STEM does not provide a method to estimate the parameters
> of the compartmental model based upon disease incidence data, does
it?
>
> Cheers,
>
> --
> Frederico Mestre
>
> Mediterranean Institute for Agriculture, Environment and Development
> The 'Rui Nabeiro' Biodiversity Chair
> Universidade de ?vora | Rua Dr. Joaquim Henrique da Fonseca 7000 ?
890
> ?vora, Portugal
> *E-mail:* mestre.frederico@xxxxxxxxx | fmestre@xxxxxxxxx *Web:*
> www.med.uevora.pt
> *ResearchGate*: https://www.researchgate.net/profile/Frederico_Mestre
> *Website*: https://geekcologist.wordpress.com
> ?
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-- 
Frederico Mestre

Mediterranean Institute for Agriculture, Environment and Development
The 'Rui Nabeiro' Biodiversity Chair
Universidade de ?vora | Rua Dr. Joaquim Henrique da Fonseca 7000 ? 890
?vora, Portugal
*E-mail:* mestre.frederico@xxxxxxxxx | fmestre@xxxxxxxxx *Web:*
www.med.uevora.pt
*ResearchGate*: https://www.researchgate.net/profile/Frederico_Mestre
??*Website*: https://geekcologist.wordpress.com
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