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TB-DURATION / mice

Mice studies reanalysis
https://tb-duration.github.io/mice/analysis.html
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Add additional data to the analysis #1

Open choisy opened 9 months ago

choisy commented 9 months ago

So far the analysis is based on table 2 of 10.1164/rccm.201103-0397OC only. Provide additional data (DOI + table or figure number) to integrate in the analysis.

TimothyMWalker commented 9 months ago

TMC is in table 2. That's Bedaquiline.

choisy commented 9 months ago

Oh right! Should I consider the 4 treatments including TMC or only some of them, in which case which ones?

TimothyMWalker commented 9 months ago

I think TMC and, out of interest, TMC + PZA. I am not sure we'll use that, but it looks quite good so maybe we should consider it for very short courses. Your model should help make that decision

choisy commented 9 months ago

There no such treatment as TMC+PZA in Table 2. The only treatments including TMC in Table 2 are: TMC, TMC12.5+RPT, TMC+RPT and TMC+RPT+PZA. Which ones should I consider in addition to TMC?

TimothyMWalker commented 9 months ago

Ah, sorry. Yes, no point in combining TMC and RPT. So just look at TMC alone please. thanks

choisy commented 9 months ago

I've added TMC to the analysis, you can check here. Of note:

  1. showing the 4 treatments on a same plot became really messy. Instead now I'm showing the 4 treatments in 4 separate subplots;
  2. TMC data do not look as good as the data for the 3 other treatments in the sense that the proportion of positive at time point 3 is higher than the proportion of positive at time point 2 (although probably not significantly different);
  3. TMC does not seem to clear CFU particularly well compared to the other treatments. Is that something that makes sense when we compare with what is happening in humans? If I remember well, one of the strong argument of the mice people to show that the mouse model is a good model is that the order of the efficacies of the drugs is the same in the humans and the mice right?