This is the data Don sent me. It looks a bit noisier to me than what we had months ago (visual inspection, I am not sure) but the signals are picked up. I wonder whether running the test for more than 100 ms will make it even better. I ran a bootstrap-like analysis (more similar to a "jackknife") resampling it 1000 times, taking half of the sample (500) randomly and the most of the branches are consistent. I can give the numbers later.
Two things are needed to be considered:
1) how the branches groups to each other and how consistent they are (the are if the branches exists and the groups remain together no matter how I resample the data)
2) how long the branches are, i.e. distance.
This is just a test, a more thorough analysis could and should be done.
Since the output of Don's tool changed, I needed to rewrite the scripts.
https://sites.google.com/site/gaviotach ... &width=800
Miguel
Cluster analysis of similarity test
Moderator: Ras
-
michiguel
- Posts: 6401
- Joined: Thu Mar 09, 2006 8:30 pm
- Location: Chicago, Illinois, USA
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Laskos
- Posts: 10948
- Joined: Wed Jul 26, 2006 10:21 pm
- Full name: Kai Laskos
Re: Cluster analysis of similarity test
Sorry, I didn't follow your earlier results, I have to get used to the chart.michiguel wrote:This is the data Don sent me. It looks a bit noisier to me than what we had months ago (visual inspection, I am not sure) but the signals are picked up. I wonder whether running the test for more than 100 ms will make it even better. I ran a bootstrap-like analysis (more similar to a "jackknife") resampling it 1000 times, taking half of the sample (500) randomly and the most of the branches are consistent. I can give the numbers later.
Two things are needed to be considered:
1) how the branches groups to each other and how consistent they are (the are if the branches exists and the groups remain together no matter how I resample the data)
2) how long the branches are, i.e. distance.
This is just a test, a more thorough analysis could and should be done.
Since the output of Don's tool changed, I needed to rewrite the scripts.
https://sites.google.com/site/gaviotach ... &width=800
Miguel
Do the distances on a branch mean something? Do the angles mean something?
Thanks,
Kai
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michiguel
- Posts: 6401
- Joined: Thu Mar 09, 2006 8:30 pm
- Location: Chicago, Illinois, USA
Re: Cluster analysis of similarity test
The length of each branch represents the "disimilarity" between points.Laskos wrote:Sorry, I didn't follow your earlier results, I have to get used to the chart.michiguel wrote:This is the data Don sent me. It looks a bit noisier to me than what we had months ago (visual inspection, I am not sure) but the signals are picked up. I wonder whether running the test for more than 100 ms will make it even better. I ran a bootstrap-like analysis (more similar to a "jackknife") resampling it 1000 times, taking half of the sample (500) randomly and the most of the branches are consistent. I can give the numbers later.
Two things are needed to be considered:
1) how the branches groups to each other and how consistent they are (the are if the branches exists and the groups remain together no matter how I resample the data)
2) how long the branches are, i.e. distance.
This is just a test, a more thorough analysis could and should be done.
Since the output of Don's tool changed, I needed to rewrite the scripts.
https://sites.google.com/site/gaviotach ... &width=800
Miguel
Do the distances on a branch mean something? Do the angles mean something?
Thanks,
Kai
The angles mean absolutely nothing. In fact, it is licit to put the plot in a draw program and move the branches around, as long as you do not change the length and the nodes. For instance
Code: Select all
A
\
\ C
\ /
o----o
/ \
/ \
/ D
B
A
\ D
\ /
\ /
o----o
/ \
/ C
/
B
A
\
\
\
o----o--D
/ \
/ C
/
B
Code: Select all
C 0 3 8 8
D 0 9 9
A 0 6
B 0The other VERY important point to take into account is: How reliable are each of the branches? For instance, all the trees above are different than this
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D
A /
\ /
\ /
o--o
/ \
/ \
/ C
/
BSo... the important point is how reliable is the connection or branch represented by o--o? What is the other possibility? if the branch is not reliable, it means that this tree is not (statistically) significantly different from the following tree
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D
A /
\ /
\ /
\ /
o
|
o
/ \
/ \
/ C
/
BTo investigate the reliability of those branches what we can do is to resample the data and recalculate the tree and ask the question: How many times do I see that branch? half of the time? that is not reliable at all and I cannot conclude anything between the relationship between A,B,C,D. But, if I see the same branch no matter how many times I resample the data, the branch becomes very reliable.
These are the numbers I got (same tree I showed before). See the numbers 1000. That means, I got the same branch 1000 out of 1000 times. I included an arrow pointing to a number that means that all komodos belong to the same family, no matter how I resample the data.
Code: Select all
very reliable!!
\_______________/
|
| +------21-Kom1.2J
| +811.0-|
| +-1000-| +------09-Kom4046
V | |
+-1000-| +-------------11-Kom4046
| |
| +--------------------00-Kom1.0
|
+406.0-| +------17-Fire12
| | +906.0-|
| | +-1000-| +------18-Robbo84
| | | |
| +907.0-| +-------------01-Hou1.5
| |
+907.0-| +--------------------19-Rybka3
| |
| | +------08-Strel18
| | +813.0-|
| | +-1000-| +------20-Rybka1
| | | |
| +-------876.0-| +-------------14-Strel2
+-1000-| |
| | +--------------------16-Rybka23
| |
| | +------03-Fruit21
| | +---------------1000-|
| | | +------04-Frui231
| | |
+938.0-| +--------1000-| +------07-Shredde
| | | +907.0-|
| | | +562.0-| +------10-gaviota
| | | | |
| | +438.0-| +-------------12-Spike1.
+-1000-| | |
| | | +--------------------02-Crit042
| | |
+------| | +------------------------------------------------06-SF1.6
| | |
| | +-------------------------------------------------------05-SF171
| |
| +--------------------------------------------------------------13-SF1.8JA
|
+---------------------------------------------------------------------15-SF191JA
Miguel