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Trouble with the code sims <- make . pps . tr ( sims , empdat , tree . topo ) #4

Open Marialejandra opened 6 years ago

Marialejandra commented 6 years ago

Hello! I am trying to finish your tutorial, however I'm having trouble with R. When I try to applied the code sims <- make . pps . tr ( sims , empdat , tree . topo ) the program is telling me that tree. topo its not found. I don´t have a lot of experience with R so I am trying to fix the problem, but ihave not been successful. Can you help me? Thank you so much!

duchene commented 6 years ago

Hi Maria,

tree.topo is an object containing a tree with the topology that you enforced during your dating analysis. One way to get this topology is by reading a tree from you BEAST output, like so:

tree.topo <- read.nexus("beastrun.trees")[[1]]

You can then try running make.pps.tr and hopefully it will work! Let me know how you go.

Cheers,

David

Marialejandra commented 6 years ago

Gracias David! I will let you know! thank you answering me so soon!

2017-10-05 20:13 GMT-03:00 duchene notifications@github.com:

Hi Maria,

tree.topo is an object containing a tree with the topology that you enforced during your dating analysis. One way to get this topology is by reading a tree from you BEAST output, like so:

tree.topo <- read.nexus("beastrun.trees")[[1]]

You can then try running make.pps.tr and hopefully it will work! Let me know how you go.

Cheers,

David

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