How to access viral loads per person in each time point

[mariaelf97]

Hello team,

Thank you for creating this great software! I was wondering how I could access the viral load/shedding for each person in the simulation at each time point.

I want to access the numbers from figure 2 in your paper:
https://pmc.ncbi.nlm.nih.gov/articles/PMC8341708/#sec002

I appreciate the clarification!

[cliffckerr]

Hi @mariaelf97, thank you for your kind words! I see you closed this issue already, but responding for posterity :) Viral load isn't one of the quantities stored by Covasim by default (five years later, I can no longer remember why not!). But you can calculate it from other quantities that are stored in the sim.people object by applying the compute_viral_load() function:
https://github.com/InstituteforDiseaseModeling/covasim/blob/main/covasim/utils.py#L39

Here's the script we used to make the figure in the paper:
https://github.com/amath-idm/covasim_methods_paper/blob/main/figs/viral_load_plot.py

Another, potentially simpler, solution would just be to define a new people.viral_load state, and then store it right after it's calculated here.

Lastly, if you're doing non-COVID modeling, you might want to take a look at our new tool Starsim, which uses the same design principles as Covasim but is much more flexible for modeling other diseases.