Friday, July 29, 2011

DIYDodecad 1.01

I've made a couple of very small changes; download links have been updated.

- I've added even more detailed instructions in the README file. If you follow the instructions carefully, you will be able to run the program. I am only assuming a very basic level of computer competence (= the ability to read and follow instructions, the ability to type, the ability to install and start programs)

- I've added a new "progress" mode in addition to the "silent" and "verbose" (default). The "progress" mode shows the temporary solutions as the program is running, so they might be fun to see how the admixture proportions converge to the final solution.

A thing to note is that if the admixture proportions appear to stay the same in successive iterations, they do not necessarily stay the same. For example, a printed 0.23% in the temporary solution may be slowly changing from 0.23001% to 0.23002% etc. With the default convergence criteria it is guaranteed that the final solution will be very close to the one received if you let it run forever.
Posted by Dienekes at 2:16 PM
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15 comments:

  1. AnonymousJuly 30, 2011 at 2:42 AM

    I did 34,643 iterations in progress mode, and the proportions were about the same. Maybe you could add multithreading.

    ReplyDelete
  2. yo mamaAugust 3, 2011 at 5:05 AM

    How do I turn on progress mode? Can you provide the command? Checked the Readme but did not see it. Thanks.

    ReplyDelete
  3. yo mamaAugust 3, 2011 at 6:35 AM

    Nevermind, I figured it out. (Edit 'dv3.par' to substitute "progress" for "verbose", then run as usual.)

    ReplyDelete
  4. AnonymousAugust 5, 2011 at 10:38 AM

    Anyone care to explain how to turn on progress mode for us "dummies"? Thanks

    ReplyDelete
  5. DienekesAugust 5, 2011 at 11:17 AM

    Anyone care to explain how to turn on progress mode for us "dummies"? Thanks


    It's in the README. And in the post above yours.

    ReplyDelete
  6. AnonymousAugust 5, 2011 at 2:18 PM

    Sorry Dienekes, I'm a newbie. The README doesn't make it clear how to "edit dv3.par". I apologize if I missed anything, but any help would be greatly appreciated.

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  7. DienekesAugust 5, 2011 at 2:19 PM

    You can use any text editor you want, such as Notepad.

    ReplyDelete
  8. ObserverAugust 7, 2011 at 4:55 PM

    I got this error: ------------------------------------------------------
    -- DIY Dodecad v 1.0 ---------------------------------
    ------------------------------------------------------
    -- Copyright (c) 2011 Dienekes Pontikos --------------
    ------------------------------------------------------
    --- More information: --------------------------------
    ----- Dienekes' Anthropology Blog --------------------
    -------- http://dienekes.blogspot.com ----------------
    ----- The Dodecad Ancestry Project -------------------
    -------- http://dodecad.blogspot.com -----------------
    ------------------------------------------------------
    At line 64 of file DIYDodecad.f file: "in.exe"
    Traceback: not available, compile with -ftrace=frame or -ftrace=full
    Fortran runtime error: System can't find file
    Warning:
    execution of commando 'DIYDodecadWin dv3.par' results Status 2

    ReplyDelete
  9. DienekesAugust 7, 2011 at 5:05 PM

    Download the whole package, not just the exe file, and follow the instructions.

    ReplyDelete
  10. ObserverAugust 7, 2011 at 9:41 PM

    I downloaded the whole package, followed the instructions and made the genotype file.

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  11. DienekesAugust 7, 2011 at 10:57 PM

    Did you change the directory in the operating system command prompt to the workng directory?

    ReplyDelete
  12. ObserverAugust 8, 2011 at 1:19 AM

    I changed it in R and pasted
    system('DIYDodecadWin dv3.par')

    ReplyDelete
  13. zig matthew jonesAugust 17, 2011 at 8:06 AM

    First, thank you for sharing your software.

    My results below in the event that anyone is interested(my wife really doesn't care)

    My results would appear to be even more diverse than I had expected (no east African though).


    FINAL ADMIXTURE PROPORTIONS:
    10095 iterations
    Log Likelihood = -1.6208452339E+05
    -----------------------------
    East_European 13.91%
    West_European 39.81%
    Mediterranean 19.33%
    Neo_African 1.21%
    West_Asian 6.48%
    South_Asian 2.92%
    Northeast_Asian 7.84%
    Southeast_Asian 3.61%
    East_African 0.00%
    Southwest_Asian 2.01%
    Northwest_African 2.46%
    Palaeo_African 0.41%

    Compare this to the results that Dr McDonald had for me

    Male Most likely fit is:

    74.3% (+- 0.3%) Europe (all Western Europe)

    and 10.6% (+- 0.1%) Mideast (all North Africa)

    and 12.5% (+- 0.4%) America (all Native (Central) American) and 2.6% (+- 0.3%) E. Asia (various subcontinents)



    Any thoughts or comments are welcome.

    ReplyDelete
  14. zig matthew jonesAugust 17, 2011 at 8:59 AM

    Also, are any of these groupings other than Northeast_Asian (7.84%) commonly indicative of Amerindian heritage?

    I don't really have another explanation for Southeast_Asian (3.61%)

    ReplyDelete
  15. Dodecad ProjectAugust 17, 2011 at 10:08 AM

    Amerindian heritage is not covered from this test. From past experiments, Amerindians tend to group with North Asians more than they do with South Asians, but really the results are unpredictable if a genome with substantial Amerindian ancestry is tested with 'dv3'.

    ReplyDelete

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