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Hyper parameters are not estimated #45

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richelbilderbeek opened this issue Jul 21, 2018 · 5 comments
Closed

Hyper parameters are not estimated #45

richelbilderbeek opened this issue Jul 21, 2018 · 5 comments

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@richelbilderbeek
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Feedback bjoelle:

the distribution hyper parameters (alpha, beta, mean etc - all except lambda) can be set with estimate = TRUE, but the xml will not be created correctly with those settings (missing distribution, operators and state sections). I think the code should not allow this setting until this functionality is fully implemented.
@richelbilderbeek richelbilderbeek mentioned this issue Jul 21, 2018
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@richelbilderbeek richelbilderbeek mentioned this issue Oct 25, 2018
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richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
Indicate which hyper parameters are not estimated, progress #45
a5bf26c
@richelbilderbeek
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bjoelle has a point there: this has been implemented and tested only partially. First step is (in the commit above) is to have a failing assert when the implementation is incomplete.

@richelbilderbeek
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On the other hand, it is partially implemented! Should I throw away the partial implementation, and rebuild it when needed, or keep it, but fail fast?

@richelbilderbeek
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Nah, bjoelle is right: I should remove the illusion of having hyper priors from the interface.

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But also here: sometimes the interface is complete...

richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
'create_param_sigma' has no illusion of a hyper parameter, progress #45
2b8759b
richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
'create_scale_param' has no illusion of a hyper parameter, progress #45
3a62d82
richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
'create_s_param' has no illusion of a hyper parameter, progress #45
139803c
richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
'create_alpha_param' has no illusion of a hyper parameter, progress #45
78d62b8
richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
'create_beta_param' has no illusion of a hyper parameter, progress #45
7891091
richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
'create_clock_rate_param' has no illusion of a hyper parameter, progr…
30dd24e 
…ess #45
richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
'create_m_param' has no illusion of a hyper parameter, progress #45
24bc6d0
richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
'create_mean_param' has no illusion of a hyper parameter, progress #45
82c5dd8
richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
'create_mu_param' has no illusion of a hyper parameter, progress #45
0aed9ee
@richelbilderbeek
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I've removed the estimate = FALSE option from the interface. The partially complete back-end I leave intact.

There are some parameters that are estimate = TRUE by default, for the GTR site model. I just leave these be.

I consider this done.

richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
Document hyper parameters are disabled, fix #45
4f0a882
@richelbilderbeek richelbilderbeek mentioned this issue Oct 25, 2018
Closed
richelbilderbeek pushed a commit that referenced this issue Oct 25, 2018
'create_rate_ct_param' has no illusion of a hyper parameter, progress #…
81fac2e 
…45
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