Question: r/m calculation with CI95%! about clonalframeml

[xavierdidelot]

When using the emsim option there is a much simpler (and better!) option to calculate the 95%CI of r/m. Each line of the file ending with suffix emsim.txtcontains sampled values of R/theta, delta and nu. Multiply these three values to get the sampled values of r/m for each line. The 95%CI is then obtained by taking the 2.5% and 97.5% quantiles of these sampled values. In R you can do this using: quantile(values,probs=c(0.025,0.975))

Yes if two 95%CI do not overlap then it suggests that there is a significant difference at the p=0.05 level.

When using embranch option things are a bit different since there will be parameter estimated for each branches.

[maesaar]

@xavierdidelot thank you!

But in principle the calculations are correct either way? By calculating as I did and also as you suggested?

[xavierdidelot]

The intervals you get using my method based on the output of emsim are more statistically valid than the ones calculated using the method you described, but otherwise yes what you described is a correct application of what I had described in other issues.

[maesaar]

Thank you again