Comments (4)
Hi! I would like to know this too, as I am having the same issue.
It would be awesome if the developers of treePL could provide a proper tutorial that would take readers through the whole process of running the prime thing first, choosing the best smoothing parameter and opt arguments and then running the actual analysis, like the developers of BEAST2 did. It is not easy to try to piece together how authors who published treePL analyses actually did their thing, because such details cannot figure in a Methods section, and contacting them to ask directly often fails (I am still waiting for answers, after quite some time...).
Many thanks!
from treepl.
Yeah I am struggling to know whether I'm doing the right steps at all, to be honest! And how to check that each has worked correctly. Do you know of any tutorials available online? I can't find anything.
from treepl.
Nah that's the problem, there is no tutorial online. You kinda have to read in-between the lines of the Methods sections of paper that used treePL and try to patch the remaining holes with the info you might find on this forum. But you never really know if what you do is the right thing, and when weird messages like this "Linear search failed" pop up there is no help for this. That's why I was asking if the developers could produce some tutorial, like the developers of BEAST2 did :)
I am planning on writing a tutorial based on my own experience once the paper I am writing using treePL is published (i.e. once my method is peer-reviewed ah ah!), but this will not happen before most likely another year, so in the meantime I am hoping that a general tutorial will pop up somewhere...
from treepl.
Thanks for the tutorial by the way ;)
from treepl.
Related Issues (20)
- Tree is invalid: missing concluding semicolon HOT 7
- segmentation fault HOT 2
- Unstable smooth values
- CV hanging HOT 1
- Writing a for loop for treepl? HOT 2
- Confidence Intervals: Bayesian vs ML
- treepl: command not found HOT 1
- Problem with mrca and tiny branch length at internal node. HOT 1
- Treepl+RaxML replicate trees HOT 1
- Installation problem
- treePL not following age calibrations HOT 4
- R script to check consistency of calibrations for 100 large trees (~3,000 taxa)? HOT 22
- Is there a license? HOT 1
- How to call treePL ?? HOT 11
- Segmentation fault (core dumped) when using prime
- Failed setting feasible start rates/dates after 10 attempts. Aborting. HOT 8
- The root time is biased towards the maximum time of the fossil which calibrated to the root. HOT 3
- Large variation among different replicates but with same parameters
- Installation issues HOT 1
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from treepl.