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Author Topic: KenN's Gen111T Generation Age Calculator  (Read 3719 times)
Mark Jost
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« on: September 03, 2012, 01:02:14 PM »

MikeW had originally created a nice TMRCA Estimator using Ken Nordtvedt's Gen7 Age calculator.  I took the liberty to integrated the new Nordtvedt Gen111T engine into Mike's Gen 7.1 Estimator and upgraded the long hand calculations to internal excel functions that provide more precision in Excel 2003 or later. The Var/VarP type functions use a two-pass process that finds the sample mean on the first pass and computes the sum of squared deviations on the second pass. Added intraclade Var & SD and a Pooled SD calculation for Interclade sigma number and variance data, added new Age info in a new Dashboard with Interclade auto iteration feature and adjustable Generation age setting. Haplotype datasets of one length can be stepped down to smaller length by selection.

I have posted a Zipped copy of the beta spreadsheet on my google documents storage.

https://docs.google.com/file/d/0By9Y3jb2fORNeUo0eWpBeGRlYkE/edit

Please let me know if there are any issues.

MJost

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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mkk
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« Reply #1 on: September 03, 2012, 02:21:01 PM »

This is probably a noobish question, who how does one download it? I tried save as, but when I tried to open it on excel it said there was some missing file. Clicking download just sent me to a redirect loop screen.
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Mark Jost
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« Reply #2 on: September 03, 2012, 02:28:26 PM »

This is probably a noobish question, who how does one download it? I tried save as, but when I tried to open it on excel it said there was some missing file. Clicking download just sent me to a redirect loop screen.

Ah, this is a Zipped (compressed) file. Once downloaded, click to open and it will show you the contents inside. Either, 1) click extract button and it will save the file to your computer, or 2) just double click and it will open in Excel leaving the file in compressed folder.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mkk
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« Reply #3 on: September 03, 2012, 02:38:51 PM »

I was able to download it after clicking on files and then download.

Before I clicked on that little grey arrow to the right of the screen.

Thanks for the help anyway.
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Mark Jost
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« Reply #4 on: September 18, 2012, 03:31:03 AM »

Y_DNA_Tools-TMRCA-Gen111T_Estimator_Mod MJost-Master New Formulas Beta2  available

Found direct from my Google Documents

https://docs.google.com/file/d/0By9Y3jb2fORNX2FjVV85bmVtWWs/edit

Intergrated Filtering now available in the Clade sheets. A Filter Mean & Modal macro must be ran to recalculate Interclade Pooled SD. Conditional (color shades indicators) Formating was removed for speed issues.


MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #5 on: October 02, 2012, 02:10:16 PM »

Updated my modified version of the Age Estimate spreadsheet revised Filtering option inside of both Clades. If Filtering is active, then a required 'Filtering' macro has to be run to re-calculate SD/VARs for Interclade use, after which the 'Interclade Age' macro needs run next. (The individual STR Variance issue is fixed as well)

https://docs.google.com/open?id=0By9Y3jb2fORNX2FjVV85bmVtWWs

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #6 on: October 03, 2012, 12:21:16 PM »

Uploaded minor update feature to unhide filtered data with a Rest button  in the two clade pages.


https://docs.google.com/open?id=0By9Y3jb2fORNX2FjVV85bmVtWWs

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
stoneman
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« Reply #7 on: October 03, 2012, 12:53:32 PM »

What is your present TMRCA estimate for R1b-Z156? I cant open any of the links that you posted as I live in the sticks without broadband.I have to go to the nearest town library.
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Mark Jost
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« Reply #8 on: October 03, 2012, 01:08:18 PM »

I just loaded a older U106 dataset from Aug and checked you request with the newest Age Estimator I have.

YrsPerGen  Count
30  N=26

Founder's Age   
Generations    StdDevInGen   YBP    +-YBP    Max
109.3   30.5   3,279.4   915.7   4,195.1

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #9 on: October 13, 2012, 11:55:32 AM »

Added a optional Confidence Calculator to investigate a difference standard deviation distribution range. Loaded MikeW's P312xL21 67 marker data set in Clade B for those who wish to calculate some ages on those subclades.

https://docs.google.com/open?id=0By9Y3jb2fORNX2FjVV85bmVtWWs

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #10 on: October 13, 2012, 02:52:02 PM »

For the P312xL21 and U106 clades I have created the following:

Y_DNA_Tools-TMRCA-Gen111T_Estimator_ModMJost-10132012_U106-P312xL21_67Markers

or download directly here:
https://docs.google.com/file/d/0By9Y3jb2fORNamQtMm9kVnBLc00/edit

This is my latest beta version of MikeW Estimator modified with KenN's Gen111T
engine and my additional mods using prefilled 67 marker U106 and P313xL21
Haplotypes. Filtering is possible in either of the Clade(X)_Hts sheet for
analysis. Please read the processing steps needed and the remaining notes and
use "as is". Stored in my Google Documents.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #11 on: October 15, 2012, 06:14:30 PM »

Modified the Interclade Pooled SD formula allowing two equal datasets to pool correctly.  I loaded MikeW's L21 111 marker data set in Clade A and B for those who wish to calculate some Interclade ages between L21 SNP clades and their subclades.

https://docs.google.com/open?id=0By9Y3jb2fORNX2FjVV85bmVtWWs

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #12 on: October 15, 2012, 07:52:18 PM »

Mike,
I am testing the  Inter and Intra Clade TMRCA's for the L513 subclade. Comments?

https://docs.google.com/open?id=0By9Y3jb2fORNM1VGWmZ6Tk1NTG8

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mike Walsh
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WWW
« Reply #13 on: October 15, 2012, 11:49:48 PM »

Mike,
I am testing the  Inter and Intra Clade TMRCA's for the L513 subclade. Comments?

https://docs.google.com/open?id=0By9Y3jb2fORNM1VGWmZ6Tk1NTG8

MJost

Thanks, Mark. I'm not that familiar with Google Docs. Is there a way to easily rotate the view of the charts?
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R1b-L21>L513(DF1)>S6365>L705.2(&CTS11744,CTS6621)
Mark Jost
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« Reply #14 on: October 16, 2012, 07:41:47 AM »

Download then Right click and rotate to view or from the menu bar.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #15 on: October 17, 2012, 11:19:50 PM »

Beta 4 out now going for gold.

https://docs.google.com/open?id=0By9Y3jb2fORNX2FjVV85bmVtWWs

MJost

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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #16 on: October 21, 2012, 05:30:04 PM »

Out of beta. V1.2 is up.

https://docs.google.com/file/d/0By9Y3jb2fORNX2FjVV85bmVtWWs/edit

MJost
Logged

148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #17 on: October 21, 2012, 09:14:36 PM »

I think I am done for now. I increased the speed of the copy process some things up in V1.3

https://docs.google.com/file/d/0By9Y3jb2fORNX2FjVV85bmVtWWs/edit

MJost
Logged

148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Mark Jost
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« Reply #18 on: October 25, 2012, 12:11:38 PM »

Small differences can be statistically ‘‘significant’’ simply because of a large sample size. Some critics of significance testing argue that confidence intervals and measures of effect size should be the focal point of research findings.

What is the best method of the two when considering variance and standard deviations of haplotypes?

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
stoneman
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« Reply #19 on: October 26, 2012, 03:55:52 AM »

Run some Native American haplotypes through your calculator and if the TMRCA is not 12,000 ybp then bin it.



Small differences can be statistically ‘‘significant’’ simply because of a large sample size. Some critics of significance testing argue that confidence intervals and measures of effect size should be the focal point of research findings.

What is the best method of the two when considering variance and standard deviations of haplotypes?

MJost
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Mark Jost
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« Reply #20 on: October 26, 2012, 08:54:51 AM »

Run some Native American haplotypes through your calculator and if the TMRCA is not 12,000 ybp then bin it.


12K would probably require a change in STRs used. I will look forward to you modifying the Gen111T to reflect that factand you can run the NA Hts and see what happens before and after the changes and see what occurs.
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
stoneman
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« Reply #21 on: October 26, 2012, 02:36:14 PM »

The fact is that the Native Americans ancestors arrived in America 12000 ybp. I dont need a calculator to work that one out.
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Mark Jost
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« Reply #22 on: October 26, 2012, 02:52:20 PM »

The fact is that the Native Americans ancestors arrived in America 12000 ybp. I dont need a calculator to work that one out.

Run some Native American haplotypes through your calculator and if the TMRCA is not 12,000 ybp then bin it.


I didnt think you would try.

MJost
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148326
Pos: Z245 L459 L21 DF13**
Neg: DF23 L513 L96 L144 Z255 Z253 DF21 DF41 (Z254 P66 P314.2 M37 M222  L563 L526 L226 L195 L193 L192.1 L159.2 L130 DF63 DF5 DF49)
WTYNeg: L555 L371 (L9/L10 L370 L302/L319.1 L554 L564 L577 P69 L626 L627 L643 L679)
Jdean
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« Reply #23 on: October 26, 2012, 03:01:10 PM »

The fact is that the Native Americans ancestors arrived in America 12000 ybp. I dont need a calculator to work that one out.

That's as maybe but it doesn't mean the MRCA is necessarily from that time, it could easily be considerably older or younger !
« Last Edit: October 26, 2012, 03:01:49 PM by Jdean » Logged

Y-DNA R-DF49*
MtDNA J1c2e
Kit No. 117897
Ysearch 3BMC9

stoneman
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« Reply #24 on: October 27, 2012, 04:11:40 AM »

So you think that I am not capable and that you are more intelligent.


The fact is that the Native Americans ancestors arrived in America 12000 ybp. I dont need a calculator to work that one out.

Run some Native American haplotypes through your calculator and if the TMRCA is not 12,000 ybp then bin it.


I didnt think you would try.

MJost
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