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BDI-pathogens / OpenABM-Covid19

OpenABM-Covid19: an agent-based model for modelling the spread of SARS-CoV-2 (coronavirus) and control interventions for the Covid-19 epidemic
GNU General Public License v3.0
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Can't find documentation of output timeseries #127

Closed fhr closed 4 years ago

fhr commented 4 years ago

The model outputs a set of timeseries for key items, e.g. total_infected, and total_case. However, I can't find a dictionary which confirms how each of these is defined. Is there such a thing in the repo somewhere?

In particular I wanted to check this in order to diagnose some unexpected behaviour: when running the model with fraction_asymptomatic set to .16 for all age groups, I get total_case to be consistently around 2.5% of total_infected. I would interpret "total_infected" as "infected including asymptomatic", while "total_case" would be "infected, symptomatic only" - so I would expect one to be .16 of the other.

p-robot commented 4 years ago

I will include this output dictionary for the time series (for the Python interface) today and the others after review from our team. They'll be stored the documentation folder with links to it from the README.md.

fhr commented 4 years ago

Thaink you Will, that would be a big help.

On 3 Jul 2020, at 16:19, Will Probert notifications@github.com wrote:

I will include this output dictionary for the time series (for the Python interface) today and the others after review from our team. They'll be stored the documentation folder with links to it from the README.md.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/BDI-pathogens/OpenABM-Covid19/issues/127#issuecomment-653593612, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFNQEG7RQ4JVRYQOKTSK5DRZXZJDANCNFSM4OP4IU3A.

roberthinch commented 4 years ago

Parameter dictionary for time-series added in PR #128.

p-robot commented 4 years ago

@fhr, total_case is tied to testing so it's intervention-specific - it'll count anyone who's had a positive test (see usage of the interventions.c::set_case() function). total_infected is anyone who's been infected so will include the states you mention.

p-robot commented 4 years ago

@fhr, there are now dictionaries of output files for the transmission file and individual file as merged in #139. These markdown files are listed in documentation/output_files.

fhr commented 4 years ago

Thanks Will, that is very useful to us.

On 9 Jul 2020, at 17:32, Will Probert notifications@github.com wrote:

@fhr https://github.com/fhr, there are now dictionaries of output files for the transmission file and individual file as merged in #139 https://github.com/BDI-pathogens/OpenABM-Covid19/pull/139. These markdown files are listed in documentation/output_files.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/BDI-pathogens/OpenABM-Covid19/issues/127#issuecomment-656228659, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAFNQEBZIN6AKWPWY6IH2PDR2XWKJANCNFSM4OP4IU3A.