Dev hiv ped 24 #31
Dev hiv ped 24 #31
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…ecks can be run repeatedly on different build ups of the model
…ts in remotes so hoping that works
This reverts commit b9eca1c.
…s like its in remotes so hoping that works" This reverts commit af795b6.
…, jeff should look at cutoffs
…ey are calculated from this population, need to add in births from hiv pos moms
…apfrog into dev_add_hivp_entrant
…fs and changed them to args to the function. Going to add these to the readme
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Also, have commented out the transmission matches tests because of the connection with demographics not matching (bc aging / natural deaths not integrated) |
…using problems in git checks
| v$paed_incid_input <- projp$nosocom_infections_04 | ||
| ## Hardcoded, this is putting all individuals in the highest cd4 category bc i think thats how the nosocomial infections work | ||
| ## v$paed_cd4_dist <- c(0.6, 0.12, 0.1, 0.09, 0.05, 0.03, 0.01) | ||
| v$paed_cd4_dist <- c(1, 0, 0, 0, 0, 0, 0) |
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@jeffeaton Looks like the nosocomial infections are all distributed into the first cd4 category, which isn't as ideal for testing this integration. Right now I'm just mirroring that
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| double dt = 1.0 / hiv_steps_per_year; | ||
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| // demography | ||
| const TensorMapX2cT basepop(p_basepop, pAG, NG); | ||
| const TensorMapX3cT basepop(p_basepop, pAG, NG, sim_years); |
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Adding in sim_years so that the pop adjust step can be done at the end of the loop
| //distribute across eligible ages, right now just going to hardcode | ||
| for(int g = 0; g < NG; g++){ | ||
| for(int af = 0; af < 5; af++){ | ||
| infections(af, g, t) = paed_incid_input(t) / 10; |
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This will need to be changed when distributing across ages correctly, matching nosocomial infections structure rn
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@r-ash, I'm not sure why these checks are now failing. To me it looks like there are just warnings. Do you see anything I should change? |
You're right they are just warnings, current settings are to fail on warning and it is worth fixing warnings. Best to fix them by qualifying calls to |
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Looks like it isn't liking the ::: import of an internal function, I found this but not quite sure how to implement drsimonj/twidlr#16 @r-ash @jeffeaton Also: https://stackoverflow.com/questions/2675502/what-does-the-symbol-mean-in-r |
As the packages it is complaining about are under our control we can choose to export those functions. ‘epp:::.parse_array’ - @jeffeaton can we export this?
If these aren't really things we don't want to export we could refactor some of this into a helper package which we then use here and elsewhere. That is a bit more faff than you probably want though so we can turn off fail on warning if this really is a pain. |
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Thanks @r-ash, sorry had parallel discussions going on this. The What has escalated it to a Warning is pulling in the @mwalte10 -- let's chat about if we want to copy that full script in. |
#24
Set up storage for stratified population of pediatric HIV (hivstrat_paeds). Have aging mapped out as well, but will wait to confirm that that is working as expected until natural deaths are working appropriately.
It looks like for nosocomial infections in spectrum all infections are put in the highest CD4 category at initial distribution, I've replicated that here.