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xavierdidelot / TransPhylo

Reconstruction of transmission trees using genomic data
http://xavierdidelot.github.io/TransPhylo/
GNU General Public License v2.0
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summary.resTransPhylo #25

Closed am-epi closed 1 year ago

am-epi commented 1 year ago

Hi,

I'm wondering what the visual output/values for summar.resTransPhylo is supposed to be? Does it provide information about the avg number of hosts identified (unsampled and sampled) across the MCMC iterations and so on? I can get that for an individual iteration using extractCTree but would be good to have an overall summary if that makes sense.

I am also having trouble getting it working... When I do just summary(res) I get the output Result from TransPhylo analysis and nothing else, when I do print.phylo(phy) by itself it gives me some info about the input tree. I have both transphylo and ape loaded but the function summary.resTransphylo isn't being recognised.

Any help would be appreciated! Thanks, Abbi

xavierdidelot commented 1 year ago

Hi Abbi,

The function summary.resTransPhylo does not do anything indeed. You can use print(res) instead which gives the parameter estimates. To get the average numbers of sampled and unsampled individuals you can use the function getIncidentCases(res)

Best wishes, Xavier

am-epi commented 1 year ago

Thanks for your help Xavier! Best wishes, Abbi