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Thread: Automated qpGraph: possibilities for the consideration of technically savvy Users?

  1. #151
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    Managed to clean up a few zero edges by moving ANE's western ancestry to branch off slightly before Goyet. It also allowed ANE to increase to more realistic levels for Iran_N and CHG.
    Still want to resolve the NE1 > NE2 zero edge.
    Not so concerned about the ANE1 > ANE2 zero edge, I could believe Yana and MA1 separating so early after the ANE component formed to have not accumulated drift with each other, especially since their Western and Eastern halves now have healthy drift edges.
     

    digraph G {
    size = "7.5,10";
    Root -> MbutiDG [ label = "69" ];
    Root -> X [ label = "69" ];
    X -> AEA [ label = "6" ];
    AEA -> MotaSG [ label = "135" ];
    AEA -> ANA [ label = "8" ];
    ANA -> B [ label = "15" ];
    B -> B1 [ label = "9" ];
    B -> C [ label = "4" ];
    ZK -> ZlatyKunSG [ label = "137" ];
    C -> E0 [ label = "4" ];
    E0 -> E1 [ label = "0" ];
    E0 -> pUST [ label = "2" ];
    pUST -> Ust_IshimDG [ label = "133" ];
    E1 -> E2 [ label = "1" ];
    E2 -> BK1 [ label = "0" ];
    E2 -> E3 [ label = "6" ];
    BK2 -> BachoKiro_IUP [ label = "140" ];
    E3 -> pTY [ label = "19" ];
    pTY -> Tianyuan_AR33K [ label = "111" ];
    E3 -> E4 [ label = "5" ];
    E4 -> Japan_Jomon [ label = "124" ];
    pONG -> OngeDG [ label = "131" ];
    E1 -> W0 [ label = "9" ];
    W0 -> W1 [ label = "1" ];
    W3 -> W6 [ label = "5" ];
    W6 -> Kostenki14 [ label = "125" ];
    W6 -> W7 [ label = "6" ];
    W7 -> SunghirSG [ label = "120" ];
    W1 -> GOY [ label = "3" ];
    GOY -> GoyetQ116_1 [ label = "125" ];
    GRV -> GRV2 [ label = "9" ];
    GRV2 -> Gravettian [ label = "116" ];
    W0 -> W5 [ label = "2" ];
    E4 -> E5 [ label = "6" ];
    ANE0 -> ANE1 [ label = "0" ];
    pYAN -> Yana_UPSG [ label = "131" ];
    ANE1 -> ANE2 [ label = "22" ];
    ANE2 -> MA1SG [ label = "108" ];
    ANE2 -> ANE3 [ label = "23" ];
    IBM2 -> Taforalt [ label = "148" ];
    B1 -> B2 [ label = "12" ];
    NE1 -> NE2 [ label = "0" ];
    NE2 -> NE3 [ label = "17" ];
    INF2 -> Iran_GanjDareh_N [ label = "128" ];
    WHG1 -> WHG2 [ label = "15" ];
    WHG4 -> Italy_GrottaContinenza_MesoSG [ label = "125" ];
    DZU1 -> DZU2 [ label = "5" ];
    DZU2 -> AHG [ label = "2" ];
    AHG -> Anatolia_Epipaleolithic [ label = "128" ];
    NAM -> Peru_Laramate_900BP [ label = "129" ];
    pCHG2 -> CHGSG [ label = "134" ];
    B1 -> ZK [ style=dotted, label = "39%" ];
    BK1 -> BK2 [ style=dotted, label = "96%" ];
    E4 -> pONG [ style=dotted, label = "60%" ];
    W1 -> W3 [ style=dotted, label = "89%" ];
    GOY -> GRV [ style=dotted, label = "45%" ];
    W5 -> ANE0 [ style=dotted, label = "85%" ];
    ANE1 -> pYAN [ style=dotted, label = "94%" ];
    AHG -> IBM1 [ style=dotted, label = "68%" ];
    IBM1 -> IBM2 [ style=dotted, label = "49%" ];
    W5 -> ACE [ style=dotted, label = "47%" ];
    ACE -> NE1 [ style=dotted, label = "40%" ];
    NE3 -> INF1 [ style=dotted, label = "78%" ];
    INF1 -> INF2 [ style=dotted, label = "87%" ];
    GRV2 -> WHG1 [ style=dotted, label = "47%" ];
    WHG2 -> WHG3 [ style=dotted, label = "82%" ];
    WHG3 -> WHG4 [ style=dotted, label = "95%" ];
    NE2 -> DZU1 [ style=dotted, label = "55%" ];
    E4 -> NAM [ style=dotted, label = "73%" ];
    NE3 -> pCHG1 [ style=dotted, label = "46%" ];
    pCHG1 -> pCHG2 [ style=dotted, label = "88%" ];
    BK1 -> ZK [ style=dotted, label = "61%" ];
    X -> BK2 [ style=dotted, label = "4%" ];
    pUST -> pONG [ style=dotted, label = "40%" ];
    B2 -> W3 [ style=dotted, label = "11%" ];
    W7 -> GRV [ style=dotted, label = "55%" ];
    E5 -> ANE0 [ style=dotted, label = "15%" ];
    pTY -> pYAN [ style=dotted, label = "6%" ];
    GOY -> IBM1 [ style=dotted, label = "32%" ];
    ANA -> IBM2 [ style=dotted, label = "51%" ];
    E5 -> ACE [ style=dotted, label = "53%" ];
    B2 -> NE1 [ style=dotted, label = "60%" ];
    DZU2 -> INF1 [ style=dotted, label = "22%" ];
    ANE3 -> INF2 [ style=dotted, label = "13%" ];
    GOY -> WHG1 [ style=dotted, label = "53%" ];
    NE2 -> WHG3 [ style=dotted, label = "18%" ];
    ANE3 -> WHG4 [ style=dotted, label = "5%" ];
    WHG2 -> DZU1 [ style=dotted, label = "45%" ];
    ANE3 -> NAM [ style=dotted, label = "27%" ];
    DZU2 -> pCHG1 [ style=dotted, label = "54%" ];
    ANE3 -> pCHG2 [ style=dotted, label = "12%" ];
    }
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

  2. The Following 4 Users Say Thank You to Kale For This Useful Post:

     etrusco (07-24-2021),  Kapisa (07-24-2021),  kolompar (07-26-2021),  VOX (07-25-2021)

  3. #152
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    Had some fun yesterday trying to optimize graphs in the shiny app, watching the scores go down for hours on the console, then the app saying no better graph found.
    Is there a way to access the shiny app's objects from outside? It crashes often and then I lose whatever I've done.

  4. #153
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    Quote Originally Posted by kolompar View Post
    Had some fun yesterday trying to optimize graphs in the shiny app, watching the scores go down for hours on the console, then the app saying no better graph found.
    Is there a way to access the shiny app's objects from outside? It crashes often and then I lose whatever I've done.
    What to you mean by 'objects'?
    Collection of 14,000 d-stats: Hidden Content Part 2: Hidden Content Part 3: Hidden Content PM me for d-stats, qpadm, qpgraph, or f3-outgroup nmonte models.

  5. #154
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    qpGraph -> Save -> check graph format 'Edge list' -> Save Graph

    This saves the graph in a tsv file.

    Later, with the same populations/data:
    qpGraph -> Load -> choose the tsv file(should be in the downloads folder if you haven't moved it IIRC)


    Then if you want to view the graph at http://viz-js.com/ instead save as 'DOT' and paste it on the website.


    Note: Haven't used the program for quite some time so can't be sure that things haven't changed in newer versions.
    Last edited by theplayer; 07-27-2021 at 09:35 PM.

  6. #155
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    Thanks, I meant in a more "technically savvy" way, like when it crashes to see if I can salvage anything.

    Quote Originally Posted by Kale View Post
    What to you mean by 'objects'?
    The stuff you work with, like in the console, you can list all objects by ls().
    Nice graph by the way, can you try your pseudo-Dzudzuana mix into WHG (and maybe even earlier West Eurasians)? From the f3s in both papers, WHG are closest to them. To me that suggests the population that moved into Europe during the LGM (and maybe earlier) and gave rise to WHGs would be Dzudzuana-like.

  7. #156
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    Quote Originally Posted by kolompar View Post
    Thanks, I meant in a more "technically savvy" way, like when it crashes to see if I can salvage anything.


    The stuff you work with, like in the console, you can list all objects by ls().
    Nice graph by the way, can you try your pseudo-Dzudzuana mix into WHG (and maybe even earlier West Eurasians)? From the f3s in both papers, WHG are closest to them. To me that suggests the population that moved into Europe during the LGM (and maybe earlier) and gave rise to WHGs would be Dzudzuana-like.

    Dzudzuana had basal eurasian while WHG do not have it. So it is the ancestor of WHG ( proto WHG) that went into the
    Caucasus not the other way round

  8. #157
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    Quote Originally Posted by etrusco View Post
    Dzudzuana had basal eurasian while WHG do not have it. So it is the ancestor of WHG ( proto WHG) that went into the
    Caucasus not the other way round
    That's just the assumption that the idea of basal was built on. We've had thousands of new ancient samples in the years since, none of them being pre-Mesolithic WHG or pure basal, making the theory (and the release of Lazaridis's paper?) less and less likely.

  9. #158
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    Quote Originally Posted by kolompar View Post
    Thanks, I meant in a more "technically savvy" way, like when it crashes to see if I can salvage anything.


    The stuff you work with, like in the console, you can list all objects by ls().
    Nice graph by the way, can you try your pseudo-Dzudzuana mix into WHG (and maybe even earlier West Eurasians)? From the f3s in both papers, WHG are closest to them. To me that suggests the population that moved into Europe during the LGM (and maybe earlier) and gave rise to WHGs would be Dzudzuana-like.
    Hmmm not sure what that is. I've never had any success with shiny, always used the command prompt.
    In that graph WHG and 'Dzudzuana' both arise from different mixes of the same two sources, so in that sense it's not WHG > Dzu or Dzu > WHG, it's a cline.
    I'm not sure about having Dzudzuana ancestry come into play earlier, I suppose if I'm going to have proto-East-Asian exist in time for Yana at 33kbp pushing it to 37kbp for Kostenki isn't too grand a leap.
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  10. #159
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    The borderline underfit between WHG and Jomon in the previous graph became more pronounced when IronGates is used in place of GrottaContinenza.
    Either some sort of proto-ANE made it's way West early on to deliver the extra East-Eurasian, or possibly it got there independently.
    It doesn't look like anything different than what's in ANE or Iran_N though. Quite a prolific population, I hope we get some ancient samples to confirm their existence or determine it's an artifact of some other phylogeny.
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  11. #160
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    Quote Originally Posted by Kale View Post
    The borderline underfit between WHG and Jomon in the previous graph became more pronounced when IronGates is used in place of GrottaContinenza.
    Either some sort of proto-ANE made it's way West early on to deliver the extra East-Eurasian, or possibly it got there independently.
    It doesn't look like anything different than what's in ANE or Iran_N though. Quite a prolific population, I hope we get some ancient samples to confirm their existence or determine it's an artifact of some other phylogeny.
    It would be strange if it were otherwise. After all IronGates this is R1b

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