Note: The functionality described in this vignette is still quite experimental. Please keep this in mind when running qpAdm analyses and be extra careful when drawing conclusions. Feedback, criticisms and suggestions on this functionality are more then welcome!

Introduction

qpAdm model fitting is a complex topic. To navigate it successfuly requires solid knowledge of the \(f\)-statistics theory first introduced by Nick Patterson and colleagues in 2012. As part of our tutorial, we have looked at a very basic overview of the qpAdm-related functionality implemented in admixr. We also talked about the most important resources for learning more about this powerful method pioneered by Iosif Lazaridis in 2015.

Recently, Harney et al. published an exciting new preprint called “Assessing the Performance of qpAdm: A Statistical Tool for Studying Population Admixture”. Before we go any further, I encourage everyone to read it and the superb tutorial/guide available as its supplementary pdf on bioRxiv. There really isn’t a better source of information on how to run and interpret qpAdm analyses.

Please, only attempt to run qpAdm if you have familiarized yoursef with all of the above-mentioned resources. I have had many people ask questions via email (not only about qpAdm but also other topics) to which the only sensible answer was - “you have to read the papers and understand the statistics first.” I know it’s frustrating but there really are no shortcuts here.

qpAdm “rotation”

If you have ever worked with qpAdm, you are well aware of the intricacies of finding the most suitable set of models that can explain the data. Among other things, we have to make a decision about the number of admixture sources and which populations are the most appropriate surrogates for those source populations (because only rarely we have sampled them directly). Furthermore, we need to carefully choose a number of so called ‘outgroup’ populations (also called ‘references’ or ‘right’ populations, depending on whom you talk to).

The preprint by Harney et al. described an interesting idea to find a set of the most appropriate models (i.e. combinations of source and outgroup populations) which has been sucessfully used in the past. They call the method a “rotating population” strategy.

This approach starts by defining a set of “candidate” populations from which we iteratively sample a defined number of “sources” of ancestry for our “target” population of interest (most commonly two or three sources). After removing the sources from the candidate list, we then define all the remaining populations as “outgroups”. Finally, we iteratively fit qpAdm models for each combination of target, sources and outgroups, extracting \(p\)-values and other statistics of interest. After finishing the exhaustive fitting of source-outgroup combinations, we examine all explored models, selecting those that seem most appropriate.

Implementation in admixr

In admixr, I have implemented a function qpAdm_rotation() which does exactly what is described paragraph with one additional feature. Given the sensitivity of qpAdm to large numbers of potential outgroups (references), for each combination of sources and outgroups we also explore models for all possible subsets of outgroups. This is to find models which are as small as possible, possibly determining which outgroups are potentially redundant and not actually needed.

Let’s say that we have a target population T and a set of candidates for potential sources and outgroups C = {a, b, c, d, e, f}. Then, if we imagine an iteration of the rotation scheme in which we fixed sources S = {a, b}, we have remaining candidates for outgroups C - S = {c, d, e, f}. The basic implementation of the rotation procedure would simply take C - S as the full set of outgroups and fitted the following model:

  • model #1: target T, sources S = {a, b} and outgroups = {c, d, e, f}

However, in admixr, we would evaluate the following models in addition to the model #1:

  • model #2: target T, sources S = {a, b} and outgroups = {c, d, e}
  • model #3: target T, sources S = {a, b} and outgroups = {c, d, f}
  • model #4: target T, sources S = {a, b} and outgroups = {c, e, f}
  • model #5: target T, sources S = {a, b} and outgroups = {d, e, f}.

Therefore, our implementation in qpAdm_rotation() explores all posible outgroup combinations, allowing us to look for the smallest model (in terms of outgroup size) that can explain our data.

Concrete example

Performing exhaustive search by rotating sources/outgroups

As an example, let’s revisit the problem of estimating the level of Neandertal ancestry in a French person from the main tutorial. We use this as an illustration because:

  1. It’s the simplest possible analysis one could do with qpAdm.
  2. It gives us a clear expectation of what the “truth” is.
  3. It gives us a clear expectation of what models we should definitely reject.

First, let’s download and install a development version of admixr to get access to the new features, and download a small example data set:

library(admixr)

snps <- eigenstrat(download_data(dirname = tempdir()))

These are the individuals for which we have genotype data:

read_ind(snps)
#> # A tibble: 12 x 3
#>    id          sex   label      
#>    <chr>       <chr> <chr>      
#>  1 Chimp       U     Chimp      
#>  2 Mbuti       U     Mbuti      
#>  3 Yoruba      U     Yoruba     
#>  4 Khomani_San U     Khomani_San
#>  5 Han         U     Han        
#>  6 Dinka       U     Dinka      
#>  7 Sardinian   U     Sardinian  
#>  8 Papuan      U     Papuan     
#>  9 French      U     French     
#> 10 Vindija     U     Vindija    
#> 11 Altai       U     Altai      
#> 12 Denisova    U     Denisova

The qpAdm_rotation() function is very simple. It accepts:

  • a name of the target population,
  • a list of candidate populations,
  • a logical parameter minimize, determining whether to perform the “minimization” of the outgroup size described in the previous section,
  • the assumed number of sources of ancestry,
  • the number of CPU cores to use for analysis (be careful with this options as many ADMIXTOOLS analyses run in parallel can consume a lot of memory!),
  • parameter fulloutput specifying whether we want to have all the “ranks” and “subsets/patterns” statistics (see the main tutorial for more information) or if we just want the proportions of ancestry and significance values for individual models (this is the default, i.e. fulloutput = FALSE).

So, let’s say we are interested in finding the proportions of archaic human ancestry in a French individual, and we also want to see what sorts of possible models we could find that match archaic introgression. We would run the following:

models <- qpAdm_rotation(
    data = snps,
    target = "French",
    candidates = c("Dinka", "Mbuti", "Yoruba", "Vindija", "Altai", "Denisova", "Chimp"),
    minimize = TRUE,
    nsources = 2,
    ncores = 2,
    fulloutput = TRUE
)

Here is what the full output looks like:

models
#> $proportions
#> # A tibble: 336 x 13
#>    model target source1 source2 outgroups noutgroups  pvalue    prop1   prop2
#>    <chr> <chr>  <chr>   <chr>   <chr>          <int>   <dbl>    <dbl>   <dbl>
#>  1 m1    French Dinka   Mbuti   Yoruba &…          3 3.37e-2    0.757   0.243
#>  2 m2    French Dinka   Mbuti   Yoruba &…          3 1.38e-2    0.774   0.226
#>  3 m3    French Dinka   Mbuti   Yoruba &…          3 1.14e-6    0.89    0.11 
#>  4 m4    French Dinka   Mbuti   Yoruba &…          3 6.85e-2    0.781   0.219
#>  5 m5    French Dinka   Mbuti   Yoruba &…          3 1.49e-5    0.885   0.115
#>  6 m6    French Dinka   Mbuti   Yoruba &…          3 9.32e-3    0.887   0.113
#>  7 m7    French Dinka   Mbuti   Vindija …          3 6.70e-2   -8.51    9.51 
#>  8 m8    French Dinka   Mbuti   Vindija …          3 2.71e-1   25.3   -24.3  
#>  9 m9    French Dinka   Mbuti   Vindija …          3 1.61e-1 -187.    188.   
#> 10 m10   French Dinka   Mbuti   Altai & …          3 8.10e-2  -30.7    31.7  
#> # … with 326 more rows, and 4 more variables: stderr1 <dbl>, stderr2 <dbl>,
#> #   nsnps_used <dbl>, nsnps_target <dbl>
#> 
#> $ranks
#> # A tibble: 672 x 9
#>    model target  rank    df chisq       tail dfdiff chisqdiff   taildiff
#>    <chr> <chr>  <dbl> <dbl> <dbl>      <dbl>  <dbl>     <dbl>      <dbl>
#>  1 m1    French     1     1  4.51 0.0337          3     -4.51 1         
#>  2 m1    French     2     0  0    1               1      4.51 0.0337    
#>  3 m10   French     1     1  6.06 0.0138          3     -6.06 1         
#>  4 m10   French     2     0  0    1               1      6.06 0.0138    
#>  5 m100  French     1     1 23.7  0.00000114      3    -23.7  1         
#>  6 m100  French     2     0  0    1               1     23.7  0.00000114
#>  7 m101  French     1     1  3.32 0.0685          3     -3.32 1         
#>  8 m101  French     2     0  0    1               1      3.32 0.0685    
#>  9 m102  French     1     1 18.8  0.0000149       3    -18.8  1         
#> 10 m102  French     2     0  0    1               1     18.8  0.0000149 
#> # … with 662 more rows
#> 
#> $subsets
#> # A tibble: 1,008 x 12
#>    model target source1 source2 pattern    wt   dof  chisq    tail prop1 prop2
#>    <chr> <chr>  <chr>   <chr>   <chr>   <dbl> <dbl>  <dbl>   <dbl> <dbl> <dbl>
#>  1 m1    French Dinka   Mbuti   00          0     1   4.51 3.37e-2 0.757 0.243
#>  2 m1    French Dinka   Mbuti   01          1     2  23.6  7.35e-6 1     0    
#>  3 m1    French Dinka   Mbuti   10          1     2 160.   0.      0     1    
#>  4 m10   French Dinka   Mbuti   00          0     1   6.06 1.38e-2 0.774 0.226
#>  5 m10   French Dinka   Mbuti   01          1     2  23.3  8.91e-6 1     0    
#>  6 m10   French Dinka   Mbuti   10          1     2 162.   0.      0     1    
#>  7 m100  French Dinka   Mbuti   00          0     1  23.7  1.14e-6 0.89  0.11 
#>  8 m100  French Dinka   Mbuti   01          1     2  28.8  5.66e-7 1     0    
#>  9 m100  French Dinka   Mbuti   10          1     2 285.   0.      0     1    
#> 10 m101  French Dinka   Mbuti   00          0     1   3.32 6.85e-2 0.781 0.219
#> # … with 998 more rows, and 1 more variable: comment <chr>

We can see a list with three components, as we would expect from any other qpAdm() run (again, see the manual page and the tutorial for description of all three elements and their meaning). The first column of each component is always named model - this contains a short identifier of each individual “rotation” run (i.e., a combination target & sources & outgroups). It’s values don’t have any particular meaning - the order is completely arbitrary!, This variable is useful for later filtering and examination of individual models in detail.

Let’s ignore the $ranks and $subsets elements for now. We will focus only on the first element, $proportions which contains the main qpAdm summary.

Examining and filtering fitted models

The $proportions table shown above contains information about all models, regardless of their plausibility. We can see that by examining the distributions of p-values (column pvalue) and admixture proportions (columns prop1 and prop2) of each evaluated model in the figure below.

Notice two things (each dot represents one examined qpAdm model):

  • Many models have inferred admixture proportions way outside the [0, 1] interval - those are clearly nonsensical.
  • Many models have very low p-values - this means these are incompatible with the data and can be rejected.
library(tidyverse)

select(models$proportions, model, pvalue, prop1, prop2) %>%
    gather(parameter, value, -model) %>%
    ggplot(aes(parameter, value)) +
    geom_jitter() +
    facet_wrap(~ parameter, scales = "free")

To make it easier to narrow down the list of all models, admixr package contains a function qpAdm_filter(). This function accepts the result of the qpAdm_rotation() function (either the fulloutput = TRUE version or the simple data frame with admixture proportions, p-values etc. produced by usingfulloutput = FALSE) and filters out models with any of the proportions outside of the [0, 1] range and with p-values lower than a specified cutoff (0.05 by default):

# filter out models which can clearly be rejected
fits <- qpAdm_filter(models)

We can verify that the filtering worked by visualizing the filtered set of models again. Note that the p-values are distributed across the range of “insigificance” (i.e., “non-rejection”) between [0.05, 1.0]. Furthermore - remember that we originally set out to find combinations of sources-outgroups that model archaic ancestry in a French individual? We can clearly see two tidy clusters of estimated ancestry proportions. One is very small (this corresponds to the Neandertal component in modern humans - we would expect about 2-3% based on many previous analyses) and one large (“modern human” component, non-Neandertal ancestry):

select(fits$proportions, model, pvalue, prop1, prop2) %>%
    gather(parameter, value, -model) %>%
    ggplot(aes(parameter, value)) +
    geom_jitter() +
    facet_wrap(~ parameter, scales = "free") +
    coord_cartesian(y = c(0, 1))

Let’s now focus only on the proportions table. We will also ignore a couple of columns for brevity. Note that we are now also completely ignoring p-values because we cannot used those for model selection - they are not statistically meaningful at this stage! Higher p-value never implies higher likelihood of the model. Finally, we order the models based on the size of the outgroup set (smaller models first):

props <- fits$proportions %>%
    arrange(noutgroups) %>%
    select(-c(target, noutgroups, stderr1, stderr2, nsnps_used, nsnps_target))

print(props, n = Inf)
#> # A tibble: 56 x 7
#>    model source1 source2  outgroups                           pvalue prop1 prop2
#>    <chr> <chr>   <chr>    <chr>                                <dbl> <dbl> <dbl>
#>  1 m81   Dinka   Chimp    Mbuti & Yoruba & Vindija            0.963  0.937 0.063
#>  2 m82   Dinka   Chimp    Mbuti & Yoruba & Altai              0.959  0.942 0.058
#>  3 m56   Dinka   Altai    Yoruba & Vindija & Chimp            0.898  0.973 0.027
#>  4 m40   Dinka   Vindija  Yoruba & Altai & Chimp              0.875  0.975 0.025
#>  5 m52   Dinka   Altai    Mbuti & Vindija & Denisova          0.829  0.977 0.023
#>  6 m183  Yoruba  Vindija  Mbuti & Altai & Denisova            0.826  0.993 0.007
#>  7 m83   Dinka   Chimp    Mbuti & Yoruba & Denisova           0.712  0.96  0.04 
#>  8 m65   Dinka   Denisova Mbuti & Yoruba & Vindija            0.712  0.96  0.04 
#>  9 m66   Dinka   Denisova Mbuti & Yoruba & Altai              0.672  0.963 0.037
#> 10 m41   Dinka   Vindija  Yoruba & Denisova & Chimp           0.603  0.97  0.03 
#> 11 m57   Dinka   Altai    Yoruba & Denisova & Chimp           0.603  0.97  0.03 
#> 12 m55   Dinka   Altai    Yoruba & Vindija & Denisova         0.599  0.974 0.026
#> 13 m199  Yoruba  Altai    Mbuti & Vindija & Denisova          0.562  0.991 0.009
#> 14 m36   Dinka   Vindija  Mbuti & Altai & Denisova            0.561  0.979 0.021
#> 15 m50   Dinka   Altai    Mbuti & Yoruba & Denisova           0.550  0.973 0.027
#> 16 m34   Dinka   Vindija  Mbuti & Yoruba & Denisova           0.548  0.973 0.027
#> 17 m49   Dinka   Altai    Mbuti & Yoruba & Vindija            0.527  0.975 0.025
#> 18 m33   Dinka   Vindija  Mbuti & Yoruba & Altai              0.504  0.977 0.023
#> 19 m51   Dinka   Altai    Mbuti & Yoruba & Chimp              0.460  0.981 0.019
#> 20 m35   Dinka   Vindija  Mbuti & Yoruba & Chimp              0.459  0.981 0.019
#> 21 m67   Dinka   Denisova Mbuti & Yoruba & Chimp              0.448  0.982 0.018
#> 22 m37   Dinka   Vindija  Mbuti & Altai & Chimp               0.400  0.977 0.023
#> 23 m58   Dinka   Altai    Vindija & Denisova & Chimp          0.367  0.972 0.028
#> 24 m39   Dinka   Vindija  Yoruba & Altai & Denisova           0.360  0.977 0.023
#> 25 m233  Yoruba  Chimp    Mbuti & Altai & Denisova            0.343  0.988 0.012
#> 26 m42   Dinka   Vindija  Altai & Denisova & Chimp            0.291  0.976 0.024
#> 27 m53   Dinka   Altai    Mbuti & Vindija & Chimp             0.290  0.974 0.026
#> 28 m38   Dinka   Vindija  Mbuti & Denisova & Chimp            0.198  0.975 0.025
#> 29 m54   Dinka   Altai    Mbuti & Denisova & Chimp            0.197  0.975 0.025
#> 30 m232  Yoruba  Chimp    Mbuti & Vindija & Denisova          0.123  0.986 0.014
#> 31 m202  Yoruba  Altai    Vindija & Denisova & Chimp          0.0983 0.974 0.026
#> 32 m68   Dinka   Denisova Mbuti & Vindija & Altai             0.0809 0.964 0.036
#> 33 m215  Yoruba  Denisova Mbuti & Vindija & Altai             0.0788 0.988 0.012
#> 34 m231  Yoruba  Chimp    Mbuti & Vindija & Altai             0.0751 0.98  0.02 
#> 35 m186  Yoruba  Vindija  Altai & Denisova & Chimp            0.0699 0.978 0.022
#> 36 m84   Dinka   Chimp    Mbuti & Vindija & Altai             0.0698 0.942 0.058
#> 37 m71   Dinka   Denisova Yoruba & Vindija & Altai            0.0687 0.96  0.04 
#> 38 m4    Dinka   Mbuti    Yoruba & Altai & Denisova           0.0685 0.781 0.219
#> 39 m87   Dinka   Chimp    Yoruba & Vindija & Altai            0.0608 0.941 0.059
#> 40 m74   Dinka   Denisova Vindija & Altai & Chimp             0.0507 0.922 0.078
#> 41 m63   Dinka   Altai    Yoruba & Vindija & Denisova & Chimp 0.788  0.973 0.027
#> 42 m59   Dinka   Altai    Mbuti & Yoruba & Vindija & Denisova 0.770  0.976 0.024
#> 43 m44   Dinka   Vindija  Mbuti & Yoruba & Altai & Chimp      0.660  0.976 0.024
#> 44 m47   Dinka   Vindija  Yoruba & Altai & Denisova & Chimp   0.612  0.976 0.024
#> 45 m43   Dinka   Vindija  Mbuti & Yoruba & Altai & Denisova   0.607  0.978 0.022
#> 46 m60   Dinka   Altai    Mbuti & Yoruba & Vindija & Chimp    0.559  0.974 0.026
#> 47 m62   Dinka   Altai    Mbuti & Vindija & Denisova & Chimp  0.433  0.975 0.025
#> 48 m45   Dinka   Vindija  Mbuti & Yoruba & Denisova & Chimp   0.426  0.974 0.026
#> 49 m61   Dinka   Altai    Mbuti & Yoruba & Denisova & Chimp   0.425  0.974 0.026
#> 50 m46   Dinka   Vindija  Mbuti & Altai & Denisova & Chimp    0.406  0.977 0.023
#> 51 m75   Dinka   Denisova Mbuti & Yoruba & Vindija & Altai    0.196  0.962 0.038
#> 52 m91   Dinka   Chimp    Mbuti & Yoruba & Vindija & Altai    0.194  0.941 0.059
#> 53 m239  Yoruba  Chimp    Mbuti & Vindija & Altai & Denisova  0.101  0.988 0.012
#> 54 m93   Dinka   Chimp    Mbuti & Yoruba & Altai & Denisova   0.0786 0.954 0.046
#> 55 m64   Dinka   Altai    Mbuti & Yoruba & Vindija & Denisov… 0.629  0.974 0.026
#> 56 m48   Dinka   Vindija  Mbuti & Yoruba & Altai & Denisova … 0.580  0.976 0.024

Fun fact: notice in the table below that there are many models in which the chimpanzee was fitted as a source of ancestry! Interestingly, qpAdm used Chimp to infer archaic human ancestry. This is because you could think of Neandertal ancestry as an “ancestral component” of a modern human genome and the qpAdm rotation procedure therefore concludes that Chimpanzee is not be an unreasonable surrogate for a source population. Of course, we know there are better sources in our candidates set - we have the archaic humans!

filter(props, source1 == "Chimp" | source2 == "Chimp")
#> # A tibble: 11 x 7
#>    model source1 source2 outgroups                          pvalue prop1 prop2
#>    <chr> <chr>   <chr>   <chr>                               <dbl> <dbl> <dbl>
#>  1 m81   Dinka   Chimp   Mbuti & Yoruba & Vindija           0.963  0.937 0.063
#>  2 m82   Dinka   Chimp   Mbuti & Yoruba & Altai             0.959  0.942 0.058
#>  3 m83   Dinka   Chimp   Mbuti & Yoruba & Denisova          0.712  0.96  0.04 
#>  4 m233  Yoruba  Chimp   Mbuti & Altai & Denisova           0.343  0.988 0.012
#>  5 m232  Yoruba  Chimp   Mbuti & Vindija & Denisova         0.123  0.986 0.014
#>  6 m231  Yoruba  Chimp   Mbuti & Vindija & Altai            0.0751 0.98  0.02 
#>  7 m84   Dinka   Chimp   Mbuti & Vindija & Altai            0.0698 0.942 0.058
#>  8 m87   Dinka   Chimp   Yoruba & Vindija & Altai           0.0608 0.941 0.059
#>  9 m91   Dinka   Chimp   Mbuti & Yoruba & Vindija & Altai   0.194  0.941 0.059
#> 10 m239  Yoruba  Chimp   Mbuti & Vindija & Altai & Denisova 0.101  0.988 0.012
#> 11 m93   Dinka   Chimp   Mbuti & Yoruba & Altai & Denisova  0.0786 0.954 0.046

Another interesting fact: notice that the rotating population procedure selected another plausible model characterizing the ancestry of the French individual. However, this of course doesn’t represent Neandertal introgression. What it might possibly represent is left as an exercise for the reader… :)

filter(props, prop1 < 0.9, prop2 < 0.9)
#> # A tibble: 1 x 7
#>   model source1 source2 outgroups                 pvalue prop1 prop2
#>   <chr> <chr>   <chr>   <chr>                      <dbl> <dbl> <dbl>
#> 1 m4    Dinka   Mbuti   Yoruba & Altai & Denisova 0.0685 0.781 0.219

Conclusions

At this stage of analysis, you would have to decide which of the models produced by qpAdm_filter() that cannot be immediately rejected are more reasonable than others and why. Possibly based on both some prior knowledge and additional statistics (such as the details information available in the full log output information shown by loginfo()). You could say that the qpAdm methodology, while rooted in strong statistics, is from a certain point as much art as it is science. Interpreting the results and finding the most appropriate models can be quite a challenge.

Happy modeling and please, do let me know if you discover bugs or missing features. My goal with this tool is to streamline qpAdm model fitting as much as possible and I can do it only with your input.

Final remarks

  1. As a reminder, keep in mind that admixr gives you tools for filtering SNPs and also grouping samples into populations on the fly! You can easily process and group samples before plugging them into qpAdm_rotation()!

  2. Also note that you can use the function loginfo() to examine the complete log output of any model by specifying the model identifier. This is helpful not only for debugging purposes but also for cases when you need a particular statistic in the full qpAdm log report which is not currently parsed by admixr:

loginfo(fits, "m40")
#> Full output log of qpAdm rotation for model 'm40':
#> ===================================================
#> 
#> qpAdm: parameter file: /var/folders/t7/9gjtb6m92flbnp930618vt3r0000gn/T//RtmpsoJhIf/qpAdm__999364930.par
#> ### THE INPUT PARAMETERS
#> ##PARAMETER NAME: VALUE
#> genotypename: /var/folders/t7/9gjtb6m92flbnp930618vt3r0000gn/T//RtmpsoJhIf/snps/snps.geno
#> snpname: /var/folders/t7/9gjtb6m92flbnp930618vt3r0000gn/T//RtmpsoJhIf/snps/snps.snp
#> indivname: /var/folders/t7/9gjtb6m92flbnp930618vt3r0000gn/T//RtmpsoJhIf/snps/snps.ind
#> popleft: /var/folders/t7/9gjtb6m92flbnp930618vt3r0000gn/T//RtmpsoJhIf/qpAdm__999364930.popleft
#> popright: /var/folders/t7/9gjtb6m92flbnp930618vt3r0000gn/T//RtmpsoJhIf/qpAdm__999364930.popright
#> allsnps: YES
#> summary: YES
#> details: YES
#> ## qpAdm version: 1201
#> seed: 414097275
#> 
#> left pops:
#> French
#> Dinka
#> Vindija
#> 
#> right pops:
#> Yoruba
#> Altai
#> Chimp
#> 
#>   0               French    1
#>   1                Dinka    1
#>   2              Vindija    1
#>   3               Yoruba    1
#>   4                Altai    1
#>   5                Chimp    1
#> jackknife block size:     0.050
#> snps: 500000  indivs: 6
#> number of blocks for block jackknife: 547
#> ## ncols: 500000
#> coverage:               French 499434
#> coverage:                Dinka 499362
#> coverage:              Vindija 497544
#> coverage:               Yoruba 499246
#> coverage:                Altai 497729
#> coverage:                Chimp 491273
#> Effective number of blocks:   490.290
#> numsnps used: 500000
#> codimension 1
#> f4info: 
#> f4rank: 1 dof:      1 chisq:     0.025 tail:          0.875038438 dofdiff:      3 chisqdiff:    -0.025 taildiff:                    1
#> B:
#>           scale     1.000 
#>           Altai     1.301 
#>           Chimp     0.554 
#> A:
#>           scale    15.252 
#>           Dinka    -0.036 
#>         Vindija     1.414 
#> 
#> 
#> full rank
#> f4info: 
#> f4rank: 2 dof:      0 chisq:     0.000 tail:                    1 dofdiff:      1 chisqdiff:     0.025 taildiff:          0.875038438
#> B:
#>           scale   421.013    10.787 
#>           Altai    -1.293     1.301 
#>           Chimp    -0.574     0.554 
#> A:
#>           scale     1.414     1.414 
#>           Dinka     1.414     0.000 
#>         Vindija     0.000     1.414 
#> 
#> 
#> best coefficients:     0.975     0.025 
#> Jackknife mean:      0.975467965     0.024532035 
#>       std. errors:     0.005     0.005 
#> 
#> error covariance (* 1,000,000)
#>         24        -24 
#>        -24         24 
#> 
#> 
#> summ: French    2      0.875038     0.975     0.025         24        -24         24 
#> 
#>     fixed pat  wt  dof     chisq       tail prob
#>            00  0     1     0.025        0.875038     0.975     0.025 
#>            01  1     2    24.294     5.30367e-06     1.000     0.000 
#>            10  1     2 23181.059               0     0.000     1.000 
#> best pat:           00         0.875038              -  -
#> best pat:           01      5.30367e-06  chi(nested):    24.269 p-value for nested model:     8.37552e-07
#> 
#> coeffs:     0.975     0.025 
#> 
#> ## dscore:: f_4(Base, Fit, Rbase, right2)
#> ## genstat:: f_4(Base, Fit, right1, right2)
#> 
#> details:                Dinka                Altai    -0.003070   -4.407893
#> details:              Vindija                Altai     0.120642  146.515551
#> dscore:                Altai f4:    -0.000037 Z:    -0.053286
#> 
#> details:                Dinka                Chimp    -0.001363   -2.294880
#> details:              Vindija                Chimp     0.051327   77.922651
#> dscore:                Chimp f4:    -0.000071 Z:    -0.121462
#> 
#> gendstat:               Yoruba                Altai    -0.053
#> gendstat:               Yoruba                Chimp    -0.121
#> gendstat:                Altai                Chimp    -0.086
#> 
#> ##end of qpAdm:        3.549 seconds cpu        0.000 Mbytes in use