Diffusion paths

[trvrb]

Could the authors elaborate in the Methods about the meaning of the lines connecting points in Figure 2 and 3? They say these represent "mean posterior diffusions paths," but I'm having trouble grasping what that means.

[trvrb]

We apologize for the lack of clarity here. We have included an additional paragraph in Methods under Implementation that describes the algorithm to estimate "mean diffusion paths".

[plemey]

Perhaps paste some of that relevant text in your response and save the reviewer of having to go look for it?

[trvrb]

We apologize for the lack of clarity here. We have included an additional paragraph in Methods under Implementation that describes the algorithm to estimate "mean diffusion paths". This paragraph reads as follows:

We summarize diffusion paths of viral lineages (Figure 2, Figure 3) by taking each virus and reconstructing x and y locations along antigenic dimensions 1 and 2 backward through time. We use MCMC to sample tip locations, but when outputting trees sample internal node locations using a peeling algorithm as described in [22]. Thus, after the MCMC is finished we have a posterior sample of 2000 trees each tagged with estimated tip locations and internal node locations. We post-processed each posterior tree by conducting a linear interpolation between parent-child node locations to arrive at x and y values at intervals of 0.05 years for each virus. Then, for each interval, x and y values are averaged across the sample of posterior trees. We draw lines between these locations to approximate mean posterior diffusion paths. As virus lineages coalesce backwards through time down the phylogeny these diffusion paths will also coalesce.