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thej022214 / corHMM

Fits a generalized form of the covarion model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as “hidden” states in a Markov process.
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rayDISC: Warning message: In prepareDataFitch(data) : NAs introduced by coercion to integer range #10

Closed Tambura10 closed 4 years ago

Tambura10 commented 4 years ago

Dear Jeremy,

first of all, thank you very much for Package ‘corHMM’ :). I've tried to perform rayDISC with to a trait with 41 states applied to polymorphic taxa (as you reported below). Unfortunately, I have obtained this:

State distribution in data: States: 1 1&3&4 1&4 10 10&2 10&26 10&4 10&4&13 10&6 11 11&1 11&15 11&4 12 12&1 13&10 14&10 15 15&11 15&19 15&19&32 15&22 15&22&2 15&22&29 15&23 15&27 15&29 15&32 15&4 15&4&32 15&6 15&8 16 17 18 18&15 18&15&10 18&19 18&4 18&8&4 19 19&10 19&18 19&32 19&33 19&4 19&6 2 2&4 20 21 24&1&4 25 27 3 3&10 3&2 3&4 31 32 34 4 4&1 4&10 4&13 4&30 5 5&1&4 5&10&4 5&11&4 5&18&19 5&34 5&4 6 6&10 6&4 7&27 7&28 8 8&2 9 9&18&19 9&19 9&4
Counts: 3 1 7 13 1 3 23 1 1 1 1 1 1 2 1 1 3 25 1 3 6 2 2 1 1 1 2 1 4 1 1 1 2 2 6 3 1 1 8 1 12 1 1 1 1 3 1 8 1 1 2 1 2 1 4 2 2 6 1 1 1 23 2 4 2 1 2 1 3 1 1 1 5 4 2 1 1 1 1 1 2 1 1 3
Initializing... Finished. Beginning thorough search... Finished. Inferring ancestral states using joint reconstruction. Kicking in arbitrary precision package Rmpfr due to very low probabilities. Kicking in arbitrary precision package Rmpfr due to very low probabilities. Warning message: In prepareDataFitch(data) : NAs introduced by coercion to integer range

What is wrong? Could you suggest me a solution, please? Thanks a lot for your attention and support

All my best Franco

jcoliver commented 4 years ago

Thank you for this, @Tambura10 . The warning is being thrown by a function in the phangorn package, but we'll take a look.

thej022214 commented 4 years ago

This is not a major warning and should run ok. But have dealt with it inside of corHMM.