Chronogram dating
17-Nov-2020 15:32
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It turns out that there are more options in the R package APE than I had previously been aware of - but unfortunately they are not all equally useful in everyday phylogenetics.
I quickly ran it with default parameters and lambda = 1, again setting root age to 50: Various parameters can be changed, but as implied above, if I want to do careful model comparison I would use chronos() anyway.
That being said, so far I had no use case for them.
A superseded but fast alternative: chronopl() This really came as a surprise as I believed that the function chronopl() had been removed from ape.
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Even today we had several cases of an inexplicable error message, and several cases of the analysis being unable to find a reasonable starting solution.
