covid19-model / simulator Goto Github PK

Hi again! When running the experiments.ipynb using a mob_sitting that is tu_settings_10_10.pk, meaning that the population is scaled down to 10x factor and sites is scaled down to 10x factor, I ran into the below error:

concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending.

Such error did not occurs when scaling down the population to 20x and 15x, only when scaling down the population to 10x (the sites is kept scaled down to 10x in all cases). any idea about why it occurs and how to solve it? Thanks in advance.

It looks like the function plotter.plot_Rt_types() was removed by commit 88328a4 which adds functions for computing the daily Rts. There are still several places in sim/experiments.ipynb that call plotter.plot_Rt_types(). Is the new function plotter.plot_daily_rts() intended to replace plotter.plot_Rt_types()?

Hi! I have a question about the tmax variable that is passed to the __push_household_exposure_infector_to_j function in dynamics.py:

It seams to me that if self.bernoulli_is_fatal[infector] is False, then tmax can be smaller than the current time, and this actually occurs fairly often while running the code (making household infections much less likely). There seems to be a similar issue in lines 762 and 1027. Can you please clarify this for me?

Thanks in advance!

In this line:

The number 24.0 could be made more clear as being the number of hours in a day.
In general, unit conversions in code can easily become error-prone when treated just as numbers.

At the very least, better to have some sort of constant like DAY_TO_HOURS = 24.0.
Even better, use a library like https://pint.readthedocs.io/en/0.11/ to handle units in an explicit way.

First, I would like to thanks you for making this agent-based simulator available with its detailed documentation. Second, I just want ask if there is a missing parameter in the example exe-inference.ipynb when calling the make_loss_function. Shouldn't we also pass the num_sites parameter?

Thanks again for your great works

hi,

There is an overflow issue when downscaling the population_per_age_group array which gives minus values to some of the age group. You might have to change the data type into int64 in town_settings_[town_name].py file.

Hello,

Your dataset was added to CoronaWhy (https://www.coronawhy.org/) Data Lake on Dataverse as a piece of common COVID-19 dataframe http://datasets.coronawhy.org/dataset.xhtml?persistentId=doi:10.5072/FK2/QHKUFM

Would you be willing to help with maintenance of your dataset in Dataverse, e.g. adding the relevant metadata and keeping the dataset up-to-date? That will help to make the dataset findable and accessible for medical science community.

Hi! I have a question about the following function, that samples transition times for asymptomatic nodes to recovery:

Is it possible that a multiplication factor from days to hours (self.tadj) is missing here?
Also because median_asymp_to_resi is expressed in days as well as all the other transition times parameters.

Thanks in advance!