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Portuguese Roman Samples qpAdm vs G25
#1
Using the same references and populations: 3 iberians IA, 2 Romans (Central/South Italian and Greek shifted) and 1 North African.

Note: The qpAdm results were made by the user eupator (TA and Eupedia user), I just sent him the target and left populations.


qpAdm


*Pass

Code:
> results$weights
# A tibble: 3 × 5
  target                      left            weight    se    z
                                         
1 Portugal_Conimbriga_Roman.SG Iberian_IA      0.726  0.103  7.05
2 Portugal_Conimbriga_Roman.SG Roman            0.217  0.131  1.66
3 Portugal_Conimbriga_Roman.SG North_African.DG 0.0563 0.0347  1.63
> results$popdrop
# A tibble: 7 × 14
  pat      wt  dof  chisq        p f4rank Iberian_IA  Roman North_African.DG feasible best  dofdiff chisqd…¹ p_nes…²
                                               
1 000      0    8  13.6 9.19e-  2      2      0.726  0.217          0.0563 TRUE    NA        NA    NA        NA


*Pass

Code:
> results$weights
# A tibble: 3 × 5
  target                                left            weight    se    z
                                                 
1 Portugal_Miroico_LateRoman_oAfrica.SG Iberian_IA        0.467 0.0916  5.10
2 Portugal_Miroico_LateRoman_oAfrica.SG Roman            0.206 0.114  1.81
3 Portugal_Miroico_LateRoman_oAfrica.SG North_African.DG  0.328 0.0302 10.8
> results$popdrop
# A tibble: 7 × 14
  pat      wt  dof  chisq        p f4rank Iberian_IA  Roman North_African.DG feasible best  dofdiff chisqd…¹ p_nes…²
                                               
1 000      0    8  10.4 2.35e-  1      2      0.467  0.206            0.328 TRUE    NA        NA    NA        NA



*Fail

Code:
> results$weights
# A tibble: 3 × 5
  target                        left            weight    se    z
                                         
1 Portugal_Miroico_LateRoman.SG Iberian_IA      0.503  0.0709  7.09
2 Portugal_Miroico_LateRoman.SG Roman            0.397  0.0898  4.42
3 Portugal_Miroico_LateRoman.SG North_African.DG 0.0996 0.0236  4.23
> results$popdrop
# A tibble: 7 × 14
  pat      wt  dof  chisq        p f4rank Iberian_IA  Roman North_African.DG feasible best  dofdiff chisqd…¹ p_nes…²
                                               
1 000      0    8  28.3 4.28e-  4      2      0.503  0.397          0.0996 TRUE    NA        NA    NA        NA



*Pass (Close call)

Code:
[/color] > results$weights
# A tibble: 3 × 5
  target                            left            weight    se    z
                                             
1 Portugal_MonteDaNora_LateRoman.SG Iberian_IA        0.403 0.0690  5.84
2 Portugal_MonteDaNora_LateRoman.SG Roman            0.395 0.0843  4.69
3 Portugal_MonteDaNora_LateRoman.SG North_African.DG  0.202 0.0226  8.95
> results$popdrop
# A tibble: 7 × 14
  pat      wt  dof  chisq        p f4rank Iberian_IA  Roman North_African.DG feasible best  dofdiff chisqd…¹ p_nes…²
                                               
1 000      0    8  15.7 4.67e-  2      2    0.403  0.395            0.202 TRUE    NA        NA    NA        NA




Global25/G25


Scaled

Target: Portugal_Conimbriga_Roman.SG
Distance: 2.0861% / 0.02086144
88.0 Iberian_IA
8.0 Roman
4.0 North_African

Target: Portugal_Miroico_LateRoman_oAfrica.SG
Distance: 2.3469% / 0.02346904
47.6 Iberian_IA
29.8 North_African
22.6 Roman

Target: Portugal_Miroico_LateRoman.SG
Distance: 1.5184% / 0.01518409
67.0 Iberian_IA
19.6 Roman
13.4 North_African

Target: Portugal_MonteDaNora_LateRoman.SG
Distance: 1.3043% / 0.01304294
45.8 Iberian_IA
34.2 Roman
20.0 North_African


Unscaled

Target: Portugal_Conimbriga_Roman.SG
Distance: 1.2275% / 0.01227499
90.0 Iberian_IA
5.8 Roman
4.2 North_African

Target: Portugal_Miroico_LateRoman_oAfrica.SG
Distance: 1.3346% / 0.01334606
48.0 Iberian_IA
34.8 North_African
17.2 Roman

Target: Portugal_Miroico_LateRoman.SG
Distance: 0.8682% / 0.00868199
66.2 Iberian_IA
20.4 North_African
13.4 Roman

Target: Portugal_MonteDaNora_LateRoman.SG
Distance: 0.6554% / 0.00655364
45.0 Iberian_IA
28.8 Roman
26.2 North_African
Senhor_Fernandes and Mulay 'Abdullah like this post
AncestryDNA (2023): 56% European, 37% Indigenous Mexican, 4% SSA & 3% MENA

AncestryDNA (2023 hack): 57.27% European, 35.81% Indigenous Mexican, 3.46% MENA & 3.45% SSA

Admixture model by I Olalde · 2019
[1] "penalty= 0.001"
[1] "Ncycles= 2000"
[1] "distance%=2.039"

        Jalisciense

Iberian EMA,48.6
Native American,34.8
Moroccan LN,8.8
Levantine EBA,4
African,3.8
Reply
#2
Global25/G25

  R+nMonte3


Unscaled

*Using the standard penalty


[1] "penalty= 0.001"
[1] "Ncycles= 1000"
[1] "distance%=1.0805"

        Portugal_Conimbriga_Roman.SG

Iberian IA,88.8
Roman,9.6
North African,1.6



[1] "penalty= 0.001"
[1] "Ncycles= 1000"
[1] "distance%=1.2432"

        Portugal_Miroico_LateRoman_oAfrica.SG

Iberian IA,41.8
North African,33.4
Roman,24.8



[1] "penalty= 0.001"
[1] "Ncycles= 1000"
[1] "distance%=0.7115"

        Portugal_Miroico_LateRoman.SG

Iberian IA,67.6
Roman,17.8
North African,14.6



[1] "penalty= 0.001"
[1] "Ncycles= 1000"
[1] "distance%=0.5698"

        Portugal_MonteDaNora_LateRoman.SG

Roman,39
Iberian IA,38.8
North African,22.2
AncestryDNA (2023): 56% European, 37% Indigenous Mexican, 4% SSA & 3% MENA

AncestryDNA (2023 hack): 57.27% European, 35.81% Indigenous Mexican, 3.46% MENA & 3.45% SSA

Admixture model by I Olalde · 2019
[1] "penalty= 0.001"
[1] "Ncycles= 2000"
[1] "distance%=2.039"

        Jalisciense

Iberian EMA,48.6
Native American,34.8
Moroccan LN,8.8
Levantine EBA,4
African,3.8
Reply
#3
Global25/G25

 R+nMonte3


Unscaled

*Now using pen=0


[1] "penalty= 0"
[1] "Ncycles= 1000"
[1] "distance%=0.8676"

        Portugal_Conimbriga_Roman.SG

Iberian IA,78.6
Roman,21.4




[1] "penalty= 0"
[1] "Ncycles= 1000"
[1] "distance%=0.9495"

        Portugal_Miroico_LateRoman_oAfrica.SG

Iberian IA,41.6
North African,32.8
Roman,25.6




[1] "penalty= 0"
[1] "Ncycles= 1000"
[1] "distance%=0.4475"

        Portugal_Miroico_LateRoman.SG

Iberian IA,65.8
North African,17.6
Roman,16.6




[1] "penalty= 0"
[1] "Ncycles= 1000"
[1] "distance%=0.2715"

        Portugal_MonteDaNora_LateRoman.SG

Iberian IA,45.8
Roman,29.8
North African,24.4
AncestryDNA (2023): 56% European, 37% Indigenous Mexican, 4% SSA & 3% MENA

AncestryDNA (2023 hack): 57.27% European, 35.81% Indigenous Mexican, 3.46% MENA & 3.45% SSA

Admixture model by I Olalde · 2019
[1] "penalty= 0.001"
[1] "Ncycles= 2000"
[1] "distance%=2.039"

        Jalisciense

Iberian EMA,48.6
Native American,34.8
Moroccan LN,8.8
Levantine EBA,4
African,3.8
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