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Topic: Bootstrapping (Read 1055 times) previous topic - next topic

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  • socrates1
Re: Bootstrapping
Reply #125
Quote
From the study:
http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
"therizinosauroids and alvarezsauroids form a clade with oviraptorosaurs and paravians exclusive of more basal coelurosaurs"

But they do not use that conclusion in their case. That polytomy is because of the unsupported nodes.

Even that is not complete because they have not shown that "Maniraptora" is also a node that should be collapsed.

One very clever way to deal with the problem of the huge polytomy is to say that support values are meaningless anyway*. The problem with that is that none of the authors of the studies make anything like that point. They go to the trouble of calculating the support values and then document the results in the Supplementary Information.
The problem is not with support values. The problem is that the authors calculate the support values and then ignore them as if they had never been calculated.
Does anyone understand that straightforward point?

* For those who are really with it, you will realize that that is an example of the "So what" stage which is a much later stage.

I am of course referring to Euparaves. The subject of the much earlier node support values is a separate subject and is related to characters vs. symplesiomorphies. I am certainly not wasting time on that. Here I am focusing on Euparaves which is an important issue/problem on its own.
The problem is that the huge polytomy means that the analysis cannot tell us anything about how the branches are related. But the authors ignore that and write as if they had some unwarranted insight about the relationships of the branches.
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
 
  • Last Edit: June 19, 2017, 11:48:54 AM by socrates1

Re: Bootstrapping
Reply #126
anyone trying to use bootstrap/jackknife as a measure of clade support is wrong. that's not what it means. hth.

Thanks, that's good to know.  What statistical metric(s) would be appropriate to use as a measure of clade support?

realistically you need to make a constraint tree and then test it against random trees using I dunno a KH or something. Node support is ridiculously hard to calculate in a meaningful way and most of the methods used to generate node support do not actually do this.

Bootstrapping and Jackknifing basically estimate how well the universe of characters that inform a specific node have been sampled. They are notoriously easy to calculate and notoriously difficult to interpret. It definitely doesn't reflect how much you should trust a node per se and doesn't tell you anything about broader trends in treespace, though.

Basically trying to treat any of these numbers as having mathematical or biological meaning is difficult to justify though.

Thanks for explaining this.

  • socrates1
Re: Bootstrapping
Reply #127
Quote
From the study:
http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
"therizinosauroids and alvarezsauroids form a clade with oviraptorosaurs and paravians exclusive of more basal coelurosaurs"

But they do not use that conclusion in their case. That polytomy is because of the unsupported nodes.

Even that is not complete because they have not shown that "Maniraptora" is also a node that should be collapsed.

One very clever way to deal with the problem of the huge polytomy is to say that support values are meaningless anyway*. The problem with that is that none of the authors of the studies make anything like that point. They go to the trouble of calculating the support values and then document the results in the Supplementary Information.
The problem is not with support values. The problem is that the authors calculate the support values and then ignore them as if they had never been calculated.
Does anyone understand that straightforward point?

* For those who are really with it, you will realize that that is an example of the "So what" stage which is a much later stage.

I am of course referring to Euparaves. The subject of the much earlier node support values is a separate subject and is related to characters vs. symplesiomorphies. I am certainly not wasting time on that. Here I am focusing on Euparaves which is an important issue/problem on its own.
The problem is that the huge polytomy means that the analysis cannot tell us anything about how the branches are related. But the authors ignore that and write as if they had some unwarranted insight about the relationships of the branches.
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
 
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
It may be that people had not caught this significant point.
We are all used to nice charts that show hypothesized nodes leading from tyrannosauroids to basal paraves
And it is hypothesized that certain bird-like characteristics were associated with those nodes. But in fact those nodes are all collapsed into Euparaves. So there is no support for ANY hypothesized assembly of bird-like characteristics.
  • Last Edit: June 19, 2017, 12:16:36 PM by socrates1

  • Faid
Re: Bootstrapping
Reply #128
Thank goodness for the support values (bootstrap/jackknife) or they could have kept bluffing forever. I am not coming up with new controversial evidence. I am simply reporting what they have documented. 
Excellelent point!

And what they have documented is a 94 jackknife value for coelurosauria (including Paraves).

Otherwise, "socrates" could have kept bluffing forever.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Bootstrapping
Reply #129
One very clever way to deal with the problem of the huge polytomy is to say that support values are meaningless anyway*.
Extremely clever way! You might need to consider it for that 94 jackknife value.
The problem with that is that none of the authors of the studies make anything like that point. They go to the trouble of calculating the support values and then document the results in the Supplementary Information.
Like that 94 jackknife value.
The problem is not with support values. The problem is that the authors calculate the support values and then ignore them as if they had never been calculated.
Like you ignore the 94 jackknife value, right?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • Faid
Re: Bootstrapping
Reply #130
The subject of the much earlier node support values is a separate subject and is related to characters vs. symplesiomorphies.
Nnnnope. If the "subject is that LOW bootstrap/jackknife values mean that nodes are not supported, then the question of that HIGH values mean is most certainly not "separate".

Refusal to address it, or resorts to special pleading, reveal nothing but dishonesty and cowardice.
I am certainly not wasting time on that.
::) See above.

But i gotta admit that trying to justify that 94 jackknife value under your proposed paradigm, would indeed be a huge waste of time.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

Re: Bootstrapping
Reply #131
94 jackknife just means that 94% of random character deletions do not affect the recovery of the node.

  • Faid
Re: Bootstrapping
Reply #132
That's a very clear and concise way of explaining it. Thanks!

Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • socrates1
Re: Bootstrapping
Reply #133
Quote
From the study:
http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
"therizinosauroids and alvarezsauroids form a clade with oviraptorosaurs and paravians exclusive of more basal coelurosaurs"

But they do not use that conclusion in their case. That polytomy is because of the unsupported nodes.

Even that is not complete because they have not shown that "Maniraptora" is also a node that should be collapsed.

One very clever way to deal with the problem of the huge polytomy is to say that support values are meaningless anyway*. The problem with that is that none of the authors of the studies make anything like that point. They go to the trouble of calculating the support values and then document the results in the Supplementary Information.
The problem is not with support values. The problem is that the authors calculate the support values and then ignore them as if they had never been calculated.
Does anyone understand that straightforward point?

* For those who are really with it, you will realize that that is an example of the "So what" stage which is a much later stage.

I am of course referring to Euparaves. The subject of the much earlier node support values is a separate subject and is related to characters vs. symplesiomorphies. I am certainly not wasting time on that. Here I am focusing on Euparaves which is an important issue/problem on its own.
The problem is that the huge polytomy means that the analysis cannot tell us anything about how the branches are related. But the authors ignore that and write as if they had some unwarranted insight about the relationships of the branches.
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
 
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
It may be that people had not caught this significant point.
We are all used to nice charts that show hypothesized nodes leading from tyrannosauroids to basal paraves
And it is hypothesized that certain bird-like characteristics were associated with each of those nodes. But in fact those nodes are all collapsed into Euparaves. So there is no support for ANY hypothesized assembly of bird-like characteristics.

Does anyone understand this? Anyone care to acknowledge it?
  • Last Edit: June 19, 2017, 02:54:07 PM by socrates1

  • Faid
Re: Bootstrapping
Reply #134
So... Your "advance warning" comes at how many posts, exactly, before you hightail it out?
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • VoxRat
  • wtactualf
Re: Bootstrapping
Reply #135
Anyone care to acknowledge it?
... asks the blowhard who - bizarrely and steadfastly - posts nestedly self-quoting post after nestedly self-quoting post without ever acknowledging so much as the presence of anyone other than himself in the thread.
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Bootstrapping
Reply #136
Quote
From the study:
http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
"therizinosauroids and alvarezsauroids form a clade with oviraptorosaurs and paravians exclusive of more basal coelurosaurs"

But they do not use that conclusion in their case. That polytomy is because of the unsupported nodes.

Even that is not complete because they have not shown that "Maniraptora" is also a node that should be collapsed.

One very clever way to deal with the problem of the huge polytomy is to say that support values are meaningless anyway*. The problem with that is that none of the authors of the studies make anything like that point. They go to the trouble of calculating the support values and then document the results in the Supplementary Information.
The problem is not with support values. The problem is that the authors calculate the support values and then ignore them as if they had never been calculated.
Does anyone understand that straightforward point?

* For those who are really with it, you will realize that that is an example of the "So what" stage which is a much later stage.

I am of course referring to Euparaves. The subject of the much earlier node support values is a separate subject and is related to characters vs. symplesiomorphies. I am certainly not wasting time on that. Here I am focusing on Euparaves which is an important issue/problem on its own.
The problem is that the huge polytomy means that the analysis cannot tell us anything about how the branches are related. But the authors ignore that and write as if they had some unwarranted insight about the relationships of the branches.
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
 
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
It may be that people had not caught this significant point.
We are all used to nice charts that show hypothesized nodes leading from tyrannosauroids to basal paraves
And it is hypothesized that certain bird-like characteristics were associated with each of those nodes. But in fact those nodes are all collapsed into Euparaves. So there is no support for ANY hypothesized assembly of bird-like characteristics.

Does anyone understand this? Anyone care to acknowledge it?

Perhaps someone will come along. Stage 1 is the most tedious. Till then we can be treated to the creativity of the insults.
  • Last Edit: June 19, 2017, 02:53:44 PM by socrates1

Re: Bootstrapping
Reply #137
No, the endlessly self-quoting tedious bullshit phase is the most tiresome. Sadly you never progress out of it.
Why do I bother?

Re: Bootstrapping
Reply #138
Quote
From the study:
http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
"therizinosauroids and alvarezsauroids form a clade with oviraptorosaurs and paravians exclusive of more basal coelurosaurs"

But they do not use that conclusion in their case. That polytomy is because of the unsupported nodes.

Even that is not complete because they have not shown that "Maniraptora" is also a node that should be collapsed.

One very clever way to deal with the problem of the huge polytomy is to say that support values are meaningless anyway*. The problem with that is that none of the authors of the studies make anything like that point. They go to the trouble of calculating the support values and then document the results in the Supplementary Information.
The problem is not with support values. The problem is that the authors calculate the support values and then ignore them as if they had never been calculated.
Does anyone understand that straightforward point?

* For those who are really with it, you will realize that that is an example of the "So what" stage which is a much later stage.

I am of course referring to Euparaves. The subject of the much earlier node support values is a separate subject and is related to characters vs. symplesiomorphies. I am certainly not wasting time on that. Here I am focusing on Euparaves which is an important issue/problem on its own.
The problem is that the huge polytomy means that the analysis cannot tell us anything about how the branches are related. But the authors ignore that and write as if they had some unwarranted insight about the relationships of the branches.
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
 
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
It may be that people had not caught this significant point.
We are all used to nice charts that show hypothesized nodes leading from tyrannosauroids to basal paraves
And it is hypothesized that certain bird-like characteristics were associated with those nodes. But in fact those nodes are all collapsed into Euparaves. So there is no support for ANY hypothesized assembly of bird-like characteristics.

Does anyone understand this? Anyone care to acknowledge it?

Perhaps someone will come along. Stage 1 is the most tedious. Till then we can be treated to the creativity of the insults.
Could you please go back to the genetic engineers from the quantum plenum phase? That is more interesting.

  • VoxRat
  • wtactualf
Re: Bootstrapping
Reply #139
Could you please go back to the genetic engineers from the quantum plenum phase? That is more interesting.
That was certainly right up there as a contender for most :rofl: -able.

Along with: cetaceans are derived from ichthyosaurs, bats (not just birds!) are derived from pterosaurs, and - this is one of my favorites - some races of humans are derived from chimps, others from gorillas.

ETA:
Oh and - almost forgot! - what psychiatrists call "schizophrenia" is actually demonic possession.
  • Last Edit: June 19, 2017, 02:57:25 PM by VoxRat
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • Faid
Re: Bootstrapping
Reply #140
No, the endlessly self-quoting tedious bullshit phase is the most tiresome. Sadly you never progress out of it.
Well there was some progress- It seems he's accepted that his posts do not belong in the Science forum.

It's understandable. If he continued to pretentiously stop posting in supposed righteous indignation, every time his threads got moved, he would never get to jerking off at his own multi-nested posts.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

Re: Bootstrapping
Reply #141
why do you guys even bother?

  • Doobie Keebler
  • Ridiculous Callipygous
Re: Bootstrapping
Reply #142

SOB

Have I missed the pretending stage?

The so what stage is not as fun.  :sadcheer:
"You know what uranium is, right? It's this thing called nuclear weapons. And other things. Like lots of things are done with uranium. Including some bad things. Nobody talks about that."

  • socrates1
Re: Bootstrapping
Reply #143
Quote
From the study:
http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
"therizinosauroids and alvarezsauroids form a clade with oviraptorosaurs and paravians exclusive of more basal coelurosaurs"

But they do not use that conclusion in their case. That polytomy is because of the unsupported nodes.

Even that is not complete because they have not shown that "Maniraptora" is also a node that should be collapsed.

One very clever way to deal with the problem of the huge polytomy is to say that support values are meaningless anyway*. The problem with that is that none of the authors of the studies make anything like that point. They go to the trouble of calculating the support values and then document the results in the Supplementary Information.
The problem is not with support values. The problem is that the authors calculate the support values and then ignore them as if they had never been calculated.
Does anyone understand that straightforward point?

* For those who are really with it, you will realize that that is an example of the "So what" stage which is a much later stage.

I am of course referring to Euparaves. The subject of the much earlier node support values is a separate subject and is related to characters vs. symplesiomorphies. I am certainly not wasting time on that. Here I am focusing on Euparaves which is an important issue/problem on its own.
The problem is that the huge polytomy means that the analysis cannot tell us anything about how the branches are related. But the authors ignore that and write as if they had some unwarranted insight about the relationships of the branches.
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
 
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
It may be that people had not caught this significant point.
We are all used to nice charts that show hypothesized nodes leading from tyrannosauroids to basal paraves
And it is hypothesized that certain bird-like characteristics were associated with each of those nodes. But in fact those nodes are all collapsed into Euparaves. So there is no support for ANY hypothesized assembly of bird-like characteristics.

Does anyone understand this? Anyone care to acknowledge it?

Perhaps someone will come along. Stage 1 is the most tedious. Till then we can be treated to the creativity of the insults.

Well it does not look like anyone will come along. It takes bravery to acknowledge what is right in front of you when others are pretending not to see it. Oh well. At least folks acknowledged the existence of the huge polytomy, so that is something.

  • VoxRat
  • wtactualf
Re: Bootstrapping
Reply #144
Quote
...
...
...
...
...
Well it does not look like anyone will come along. It takes bravery to acknowledge what is right in front of you when others are pretending not to see it. Oh well. At least folks acknowledged the existence of the huge polytomy, so that is something.
Well, Socks...
As you know, when the student is ready, The Teacher will appear.
It appears these students are just not ready.  :(
The Teacher appears to be squandering his precious time.
Have you checked in with Yann lately?
Perhaps he's finally ready.  :dunno:

"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins

  • socrates1
Re: Bootstrapping
Reply #145
Quote
From the study:
http://www.cell.com/current-biology/fulltext/S0960-9822(14)01047-1
"therizinosauroids and alvarezsauroids form a clade with oviraptorosaurs and paravians exclusive of more basal coelurosaurs"

But they do not use that conclusion in their case. That polytomy is because of the unsupported nodes.

Even that is not complete because they have not shown that "Maniraptora" is also a node that should be collapsed.

One very clever way to deal with the problem of the huge polytomy is to say that support values are meaningless anyway*. The problem with that is that none of the authors of the studies make anything like that point. They go to the trouble of calculating the support values and then document the results in the Supplementary Information.
The problem is not with support values. The problem is that the authors calculate the support values and then ignore them as if they had never been calculated.
Does anyone understand that straightforward point?

* For those who are really with it, you will realize that that is an example of the "So what" stage which is a much later stage.

I am of course referring to Euparaves. The subject of the much earlier node support values is a separate subject and is related to characters vs. symplesiomorphies. I am certainly not wasting time on that. Here I am focusing on Euparaves which is an important issue/problem on its own.
The problem is that the huge polytomy means that the analysis cannot tell us anything about how the branches are related. But the authors ignore that and write as if they had some unwarranted insight about the relationships of the branches.
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
 
For example the cladistic analysis can tell us nothing about the assembly of bird-like characteristics. It is all one blob at Euparaves. That is all the cladistic analysis can tell us.
It may be that people had not caught this significant point.
We are all used to nice charts that show hypothesized nodes leading from tyrannosauroids to basal paraves
And it is hypothesized that certain bird-like characteristics were associated with each of those nodes. But in fact those nodes are all collapsed into Euparaves. So there is no support for ANY hypothesized assembly of bird-like characteristics.

Does anyone understand this? Anyone care to acknowledge it?

Perhaps someone will come along. Stage 1 is the most tedious. Till then we can be treated to the creativity of the insults.

Well it does not look like anyone will come along. It takes bravery to acknowledge what is right in front of you when others are pretending not to see it. Oh well. At least folks acknowledged the existence of the huge polytomy, so that is something.

Feel free to keep up the silly insults. It does not really distract from your lack of bravery but go ahead.

  • Faid
Re: Bootstrapping
Reply #146
Still here?

Man, that "advance warning" Was really given in advance.

And speaking of "lack of bravery"... 94%.
Who even made the rule that we cannot group ducks and fish together for the simple reason that they are both aquatic? If I want to group them that way and it serves my purpose then I can jolly well do it however I want to and it is still a nested hierarchy and you can't tell me that it's not.

  • VoxRat
  • wtactualf
Re: Bootstrapping
Reply #147
"I understand Donald Trump better than many people because I really am a lot like him." - Dave Hawkins