qp3pop unique_only does not work as expected

[RvV1979]

I am running qp3pop to assess admixture across a set of populations. However, when I specify the same population set for pop1, pop2, and pop3, I get redundant combinations such as, e.g. f3(A;A,A) and both f3(A;B,C) and f3(A;C,B). Setting unique_only = TRUE has no effect on this.

Short reproducible example:

library("admixtools")

pop1 = c('Chimp.REF', 'Mbuti.DG', 'Russia_Ust_Ishim.DG')
pop2 = c('Chimp.REF', 'Mbuti.DG', 'Russia_Ust_Ishim.DG')
pop3 = c('Chimp.REF', 'Mbuti.DG', 'Russia_Ust_Ishim.DG')
qp3pop(example_f2_blocks, pop1, pop2, pop3, unique_only = TRUE)

Result:

# A tibble: 27 × 7
   pop1      pop2                pop3                  est       se     z     p
   <chr>     <chr>               <chr>               <dbl>    <dbl> <dbl> <dbl>
 1 Chimp.REF Chimp.REF           Chimp.REF           0     0         NaN    NaN
 2 Chimp.REF Chimp.REF           Mbuti.DG            0     0         NaN    NaN
 3 Chimp.REF Chimp.REF           Russia_Ust_Ishim.DG 0     0         NaN    NaN
 4 Chimp.REF Mbuti.DG            Chimp.REF           0     0         NaN    NaN
 5 Chimp.REF Mbuti.DG            Mbuti.DG            0.205 0.000606  339.     0
 6 Chimp.REF Mbuti.DG            Russia_Ust_Ishim.DG 0.193 0.000587  329.     0
 7 Chimp.REF Russia_Ust_Ishim.DG Chimp.REF           0     0         NaN    NaN
 8 Chimp.REF Russia_Ust_Ishim.DG Mbuti.DG            0.193 0.000587  329.     0
 9 Chimp.REF Russia_Ust_Ishim.DG Russia_Ust_Ishim.DG 0.257 0.00202   127.     0
10 Mbuti.DG  Chimp.REF           Chimp.REF           0.205 0.000606  339.     0
#  17 more rows
#  Use `print(n = ...)` to see more rows

Expected result:

# A tibble: 3 × 7
   pop1                pop2                pop3                   est       se     z         p
   <chr>               <chr>               <chr>                <dbl>    <dbl> <dbl>     <dbl>
 1 Chimp.REF           Mbuti.DG            Russia_Ust_Ishim.DG 0.193  0.000587 329.  0        
 2 Mbuti.DG            Chimp.REF           Russia_Ust_Ishim.DG 0.0118 0.000487  24.3 4.62e-130
 3 Russia_Ust_Ishim.DG Chimp.REF           Mbuti.DG            0.0635 0.00187   34.0 4.43e-253

[uqrmaie1]

The unique_only option is only effective when only pop1 is defined:

> qp3pop(example_f2_blocks, pop1, unique_only = FALSE) %>% nrow()
[1] 27
> qp3pop(example_f2_blocks, pop1, unique_only = TRUE) %>% nrow()
[1] 3

If pop1, pop2, and pop3 are all defined, it will ignore unique_only and give you all possible combinations.

[RvV1979]

Thanks for the clarification. Perhaps writing this in the qp3pop help page can help prevent similar confusion for other users.