Problems calculating the CI and RI index

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ENRIQUE TORRES PARISH

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Jul 16, 2024, 7:16:35 AM7/16/24
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Hi everybody. I'm having some problems trying to calculate the consistency index (CI) and retention Index (RI). I know that I have to use the stats.run but for some reason I don't have the extension, instead I have the aquickie.run but it does't do the same job. 
May be it's because the 1.6. version was incomplete by the time I dowloaded, I honestly don't know. How can I dowloud the stats.run for the 1.6?. 
By the way if there is an other method to calculate the CI and RI, pls let me know, I'm still figuring out how to work with TNT

René Dederichs

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Jul 16, 2024, 11:10:09 AM7/16/24
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Hello enrique, 

have you tried to 'open' the run data? Normally when i use open file > choose the .run data it should work.

Otherwise perhaps a new download would solve the problem.
Cheers

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Nick Matzke

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Jul 16, 2024, 7:31:35 PM7/16/24
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Hi!

stats.run and many (not all) of the old scripts available on the defunct TNT wiki are here:

Cheers,
Nick


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Pedro Peñaherrera

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Feb 17, 2025, 8:28:55 PMFeb 17
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Hi,

Following the second question....is there any other method to calculate the CI and RI? I'm interested in calculating both indexes per character but when I run the stats I only get the value of my tree, I saw that in some conversations this script should also indicate the CI and RI of each character. 

Hope anyone can help me.

P

Camilo

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Feb 19, 2025, 2:48:54 PMFeb 19
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Hi Pedro,

Here you have two scripts to do it:

Edward SIddall

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Feb 20, 2025, 4:03:04 PMFeb 20
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You can always do this yourself character by character. Minsteps = number of states. Maxsteps is found from optimizing on a fully unresolved hard-polytomy bush from tr. Observed steps is, well, steps observed in (say) best tree
CI = min/obs
RI = (max-obs)/(max-min)

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