Do we need more than 2 cycles

[XingerTang]

AlphaImpute2 version: commit f9e40bd
Cycle here refers to the input option cycles

Unlike AlphaPeel, AlphaImpute2 results converge really fast.

• For the combined modes, there is no difference between the 1st cycle result and the 5th cycle result, except for the decrease in the segregation probability Gen2 accuracy as the number of cycles increases, which is related to issue Possble improvements in segregation outputs #54.
• For ped_only, more cycles do improve the output accuracy. But the difference between the 1st cycle result and the 5th cycle result is small, and the difference between the 2nd cycle result and the 5th cycle result is negligible.

pop_only is irrelevant here because it is controlled by the n_phasing_cycles.

The following are the results from the accuracy tests by running 5 cycles:

(phase) xtang3@S37-50MAQ05D AlphaImpute2 % pytest tests/accuracy_tests/run_accu_test.py
=================================================================================== test session starts ===================================================================================
platform darwin -- Python 3.11.11, pytest-9.0.1, pluggy-1.6.0
benchmark: 5.2.3 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /Users/xtang3/AlphaImpute2
configfile: pyproject.toml
plugins: benchmark-5.2.3
collected 3 items                                                                                                                                                                         

tests/accuracy_tests/run_accu_test.py ...                                                                                                                                           [100%]

===================================================================================== Marker Accuracy =====================================================================================
---------------------------------------------------------------------------------------- genotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.953                0.946                0.966                0.970                0.963                0.925                pop_only                            
2                    0.768                0.517                0.773                0.991                0.994                0.988                ped_only                            
3                    0.980                0.940                0.992                0.994                0.994                0.988                combined                            
--------------------------------------------------------------------------------------- haplotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.473                0.432                0.557                0.439                0.475                0.460                pop_only                            
2                    0.684                0.194                0.761                0.988                0.991                0.984                ped_only                            
3                    0.881                0.453                0.988                0.992                0.991                0.984                combined                            
--------------------------------------------------------------------------------------- segregation ---------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.839                nan                  nan                  0.973                0.970                0.962                ped_only                            
3                    0.697                nan                  -0.115               0.974                0.970                0.962                combined                            
=================================================================================== Individual Accuracy ===================================================================================
---------------------------------------------------------------------------------------- genotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.981                0.977                0.985                0.987                0.985                0.970                pop_only                            
2                    0.896                0.602                0.890                0.995                0.997                0.995                ped_only                            
3                    0.993                0.978                0.997                0.997                0.997                0.995                combined                            
--------------------------------------------------------------------------------------- haplotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.668                0.644                0.719                0.645                0.670                0.663                pop_only                            
2                    0.846                0.418                0.833                0.992                0.995                0.990                ped_only                            
3                    0.926                0.656                0.993                0.995                0.995                0.990                combined                            
--------------------------------------------------------------------------------------- segregation ---------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.930                nan                  nan                  0.943                0.936                0.909                ped_only                            
3                    0.676                nan                  -0.098               0.947                0.936                0.909                combined                            
=========================================================================== Marker Accuracy (Order by accuracy) ===========================================================================
---------------------------------------------------------------------------------------- genotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.980                0.940                0.992                0.994                0.994                0.988                combined                            
1                    0.953                0.946                0.966                0.970                0.963                0.925                pop_only                            
2                    0.768                0.517                0.773                0.991                0.994                0.988                ped_only                            
--------------------------------------------------------------------------------------- haplotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.881                0.453                0.988                0.992                0.991                0.984                combined                            
2                    0.684                0.194                0.761                0.988                0.991                0.984                ped_only                            
1                    0.473                0.432                0.557                0.439                0.475                0.460                pop_only                            
--------------------------------------------------------------------------------------- segregation ---------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.839                nan                  nan                  0.973                0.970                0.962                ped_only                            
3                    0.697                nan                  -0.115               0.974                0.970                0.962                combined                            
========================================================================= Individual Accuracy (Order by accuracy) =========================================================================
---------------------------------------------------------------------------------------- genotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.993                0.978                0.997                0.997                0.997                0.995                combined                            
1                    0.981                0.977                0.985                0.987                0.985                0.970                pop_only                            
2                    0.896                0.602                0.890                0.995                0.997                0.995                ped_only                            
--------------------------------------------------------------------------------------- haplotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.926                0.656                0.993                0.995                0.995                0.990                combined                            
2                    0.846                0.418                0.833                0.992                0.995                0.990                ped_only                            
1                    0.668                0.644                0.719                0.645                0.670                0.663                pop_only                            
--------------------------------------------------------------------------------------- segregation ---------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.930                nan                  nan                  0.943                0.936                0.909                ped_only                            
3                    0.676                nan                  -0.098               0.947                0.936                0.909                combined                            

--------------------------------------------------------------------------------- benchmark: 3 tests ---------------------------------------------------------------------------------
Name (time in s)            Min                Max               Mean            StdDev             Median               IQR            Outliers     OPS            Rounds  Iterations
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_accu[ped_only]     18.3131 (1.0)      18.8005 (1.0)      18.5368 (1.0)      0.2136 (1.0)      18.5616 (1.0)      0.3821 (1.0)           2;0  0.0539 (1.0)           5           1
test_accu[pop_only]     19.7242 (1.08)     21.2678 (1.13)     20.3231 (1.10)     0.6958 (3.26)     19.9486 (1.07)     1.1689 (3.06)          1;0  0.0492 (0.91)          5           1
test_accu[combined]     27.1467 (1.48)     32.9407 (1.75)     31.1107 (1.68)     2.4271 (11.36)    32.0987 (1.73)     3.2451 (8.49)          1;0  0.0321 (0.60)          5           1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Legend:
  Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile.
  OPS: Operations Per Second, computed as 1 / Mean
============================================================================== 3 passed in 496.52s (0:08:16) ==============================================================================

Results for 1 cycle:

(phase) xtang3@S37-50MAQ05D AlphaImpute2 % pytest tests/accuracy_tests/run_accu_test.py
=================================================================================== test session starts ===================================================================================
platform darwin -- Python 3.11.11, pytest-9.0.1, pluggy-1.6.0
benchmark: 5.2.3 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /Users/xtang3/AlphaImpute2
configfile: pyproject.toml
plugins: benchmark-5.2.3
collected 3 items                                                                                                                                                                         

tests/accuracy_tests/run_accu_test.py ...                                                                                                                                           [100%]

===================================================================================== Marker Accuracy =====================================================================================
---------------------------------------------------------------------------------------- genotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.953                0.946                0.966                0.970                0.963                0.925                pop_only                            
2                    0.767                0.517                0.773                0.984                0.994                0.988                ped_only                            
3                    0.980                0.940                0.992                0.994                0.994                0.988                combined                            
--------------------------------------------------------------------------------------- haplotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.473                0.432                0.557                0.439                0.475                0.460                pop_only                            
2                    0.682                0.194                0.760                0.981                0.991                0.984                ped_only                            
3                    0.882                0.461                0.988                0.992                0.991                0.984                combined                            
--------------------------------------------------------------------------------------- segregation ---------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.836                nan                  nan                  0.963                0.970                0.962                ped_only                            
3                    0.702                nan                  -0.093               0.974                0.970                0.962                combined                            
=================================================================================== Individual Accuracy ===================================================================================
---------------------------------------------------------------------------------------- genotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.981                0.977                0.985                0.987                0.985                0.970                pop_only                            
2                    0.895                0.602                0.890                0.992                0.997                0.995                ped_only                            
3                    0.993                0.978                0.996                0.997                0.997                0.995                combined                            
--------------------------------------------------------------------------------------- haplotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.668                0.644                0.719                0.645                0.670                0.663                pop_only                            
2                    0.845                0.418                0.832                0.988                0.995                0.990                ped_only                            
3                    0.927                0.661                0.993                0.995                0.995                0.990                combined                            
--------------------------------------------------------------------------------------- segregation ---------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.925                nan                  nan                  0.928                0.936                0.909                ped_only                            
3                    0.681                nan                  -0.076               0.947                0.936                0.909                combined                            
=========================================================================== Marker Accuracy (Order by accuracy) ===========================================================================
---------------------------------------------------------------------------------------- genotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.980                0.940                0.992                0.994                0.994                0.988                combined                            
1                    0.953                0.946                0.966                0.970                0.963                0.925                pop_only                            
2                    0.767                0.517                0.773                0.984                0.994                0.988                ped_only                            
--------------------------------------------------------------------------------------- haplotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.882                0.461                0.988                0.992                0.991                0.984                combined                            
2                    0.682                0.194                0.760                0.981                0.991                0.984                ped_only                            
1                    0.473                0.432                0.557                0.439                0.475                0.460                pop_only                            
--------------------------------------------------------------------------------------- segregation ---------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.836                nan                  nan                  0.963                0.970                0.962                ped_only                            
3                    0.702                nan                  -0.093               0.974                0.970                0.962                combined                            
========================================================================= Individual Accuracy (Order by accuracy) =========================================================================
---------------------------------------------------------------------------------------- genotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.993                0.978                0.996                0.997                0.997                0.995                combined                            
1                    0.981                0.977                0.985                0.987                0.985                0.970                pop_only                            
2                    0.895                0.602                0.890                0.992                0.997                0.995                ped_only                            
--------------------------------------------------------------------------------------- haplotypes ----------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.927                0.661                0.993                0.995                0.995                0.990                combined                            
2                    0.845                0.418                0.832                0.988                0.995                0.990                ped_only                            
1                    0.668                0.644                0.719                0.645                0.670                0.663                pop_only                            
--------------------------------------------------------------------------------------- segregation ---------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.925                nan                  nan                  0.928                0.936                0.909                ped_only                            
3                    0.681                nan                  -0.076               0.947                0.936                0.909                combined                            

--------------------------------------------------------------------------------- benchmark: 3 tests ---------------------------------------------------------------------------------
Name (time in s)            Min                Max               Mean            StdDev             Median               IQR            Outliers     OPS            Rounds  Iterations
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_accu[ped_only]     15.8897 (1.0)      16.9678 (1.0)      16.3435 (1.0)      0.5689 (1.0)      15.9823 (1.0)      1.0562 (1.0)           2;0  0.0612 (1.0)           5           1
test_accu[pop_only]     18.4243 (1.16)     22.0725 (1.30)     19.8692 (1.22)     1.4507 (2.55)     19.9909 (1.25)     2.0114 (1.90)          1;0  0.0503 (0.82)          5           1
test_accu[combined]     27.9739 (1.76)     31.7890 (1.87)     29.9634 (1.83)     1.7343 (3.05)     30.7651 (1.92)     3.0470 (2.88)          2;0  0.0334 (0.55)          5           1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Legend:
  Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile.
  OPS: Operations Per Second, computed as 1 / Mean
============================================================================== 3 passed in 471.91s (0:07:51) ==============================================================================

Results for 2 cycles:

(phase) xtang3@S37-50MAQ05D AlphaImpute2 % pytest tests/accuracy_tests/run_accu_test.py
=================================================================================== test session starts ===================================================================================
platform darwin -- Python 3.11.11, pytest-9.0.1, pluggy-1.6.0
benchmark: 5.2.3 (defaults: timer=time.perf_counter disable_gc=False min_rounds=5 min_time=0.000005 max_time=1.0 calibration_precision=10 warmup=False warmup_iterations=100000)
rootdir: /Users/xtang3/AlphaImpute2
configfile: pyproject.toml
plugins: benchmark-5.2.3
collected 3 items                                                                                                                                                                         

tests/accuracy_tests/run_accu_test.py ...                                                                                                                                                   [100%]

========================================================================================= Marker Accuracy =========================================================================================
-------------------------------------------------------------------------------------------- genotypes --------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.953                0.946                0.966                0.970                0.963                0.925                pop_only                            
2                    0.768                0.517                0.773                0.989                0.994                0.988                ped_only                            
3                    0.980                0.940                0.992                0.994                0.994                0.988                combined                            
------------------------------------------------------------------------------------------- haplotypes --------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.473                0.432                0.557                0.439                0.475                0.460                pop_only                            
2                    0.683                0.194                0.760                0.987                0.991                0.984                ped_only                            
3                    0.882                0.458                0.988                0.992                0.991                0.984                combined                            
------------------------------------------------------------------------------------------- segregation -------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.838                nan                  nan                  0.972                0.970                0.962                ped_only                            
3                    0.700                nan                  -0.102               0.974                0.970                0.962                combined                            
======================================================================================= Individual Accuracy =======================================================================================
-------------------------------------------------------------------------------------------- genotypes --------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.981                0.977                0.985                0.987                0.985                0.970                pop_only                            
2                    0.896                0.602                0.890                0.995                0.997                0.995                ped_only                            
3                    0.993                0.978                0.996                0.997                0.997                0.995                combined                            
------------------------------------------------------------------------------------------- haplotypes --------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
1                    0.668                0.644                0.719                0.645                0.670                0.663                pop_only                            
2                    0.845                0.418                0.833                0.991                0.995                0.990                ped_only                            
3                    0.927                0.659                0.993                0.995                0.995                0.990                combined                            
------------------------------------------------------------------------------------------- segregation -------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.930                nan                  nan                  0.943                0.936                0.909                ped_only                            
3                    0.679                nan                  -0.086               0.947                0.936                0.909                combined                            
=============================================================================== Marker Accuracy (Order by accuracy) ===============================================================================
-------------------------------------------------------------------------------------------- genotypes --------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.980                0.940                0.992                0.994                0.994                0.988                combined                            
1                    0.953                0.946                0.966                0.970                0.963                0.925                pop_only                            
2                    0.768                0.517                0.773                0.989                0.994                0.988                ped_only                            
------------------------------------------------------------------------------------------- haplotypes --------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.882                0.458                0.988                0.992                0.991                0.984                combined                            
2                    0.683                0.194                0.760                0.987                0.991                0.984                ped_only                            
1                    0.473                0.432                0.557                0.439                0.475                0.460                pop_only                            
------------------------------------------------------------------------------------------- segregation -------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.838                nan                  nan                  0.972                0.970                0.962                ped_only                            
3                    0.700                nan                  -0.102               0.974                0.970                0.962                combined                            
============================================================================= Individual Accuracy (Order by accuracy) =============================================================================
-------------------------------------------------------------------------------------------- genotypes --------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.993                0.978                0.996                0.997                0.997                0.995                combined                            
1                    0.981                0.977                0.985                0.987                0.985                0.970                pop_only                            
2                    0.896                0.602                0.890                0.995                0.997                0.995                ped_only                            
------------------------------------------------------------------------------------------- haplotypes --------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
3                    0.927                0.659                0.993                0.995                0.995                0.990                combined                            
2                    0.845                0.418                0.833                0.991                0.995                0.990                ped_only                            
1                    0.668                0.644                0.719                0.645                0.670                0.663                pop_only                            
------------------------------------------------------------------------------------------- segregation -------------------------------------------------------------------------------------------
Test Num             Population Accu      Gen1 Accu            Gen2 Accu            Gen3 Accu            Gen4 Accu            Gen5 Accu            Test Name                           
2                    0.930                nan                  nan                  0.943                0.936                0.909                ped_only                            
3                    0.679                nan                  -0.086               0.947                0.936                0.909                combined                            

--------------------------------------------------------------------------------- benchmark: 3 tests ---------------------------------------------------------------------------------
Name (time in s)            Min                Max               Mean            StdDev             Median               IQR            Outliers     OPS            Rounds  Iterations
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
test_accu[ped_only]     16.1023 (1.0)      17.1375 (1.0)      16.5677 (1.0)      0.4485 (1.0)      16.5107 (1.0)      0.7988 (1.49)          2;0  0.0604 (1.0)           5           1
test_accu[pop_only]     17.2555 (1.07)     19.1074 (1.11)     18.7005 (1.13)     0.8090 (1.80)     19.0624 (1.15)     0.5370 (1.0)           1;1  0.0535 (0.89)          5           1
test_accu[combined]     26.9551 (1.67)     34.3877 (2.01)     30.2094 (1.82)     2.8472 (6.35)     30.1499 (1.83)     3.9795 (7.41)          2;0  0.0331 (0.55)          5           1
--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------

Legend:
  Outliers: 1 Standard Deviation from Mean; 1.5 IQR (InterQuartile Range) from 1st Quartile and 3rd Quartile.
  OPS: Operations Per Second, computed as 1 / Mean
================================================================================== 3 passed in 468.40s (0:07:48) ==================================================================================

This does not only apply to the accuracy test example, for the combined imputation run for the example dataset in the example/ folder, the peeling times are suspiciously fast and similar for the imputation cycle 2 onwards. Here are the logs for the combined imputation:

       Initial Pedigree Imputation        
------------------------------------------
Number of peeling cycles: 4
Final cutoff before population imputation: 0.9

Imputation cycle 1
Peel down: 3.74 seconds
Peel up: 2.52 seconds

Imputation cycle 2
Peel down: 0.01 seconds
Peel up: 0.02 seconds

Imputation cycle 3
Peel down: 0.01 seconds
Peel up: 0.02 seconds

Imputation cycle 4
Peel down: 0.01 seconds
Peel up: 0.02 seconds
Core peeling cycles: 6.35 seconds
Heuristic Peeling: 7.56 seconds

And

        Final Pedigree Imputation         
------------------------------------------
Number of peeling cycles: 4
Final cutoff: 0.1

Imputation cycle 1
Peel down: 0.01 seconds
Peel up: 0.02 seconds

Imputation cycle 2
Peel down: 0.01 seconds
Peel up: 0.02 seconds

Imputation cycle 3
Peel down: 0.01 seconds
Peel up: 0.02 seconds

Imputation cycle 4
Peel down: 0.01 seconds
Peel up: 0.02 seconds
Core peeling cycles: 0.12 seconds
Heuristic Peeling: 0.20 seconds

We can see the times are all 0.01 seconds for peel down, and 0.02 seconds for peel up.

The same applies to the pedigree-only imputation:

         Pedigree Imputation Only         
------------------------------------------
Number of peeling cycles: 4
Final cutoff: 0.98

Imputation cycle 1
Peel down: 3.63 seconds
Peel up: 2.52 seconds

Imputation cycle 2
Peel down: 0.01 seconds
Peel up: 0.02 seconds

Imputation cycle 3
Peel down: 0.01 seconds
Peel up: 0.02 seconds

Imputation cycle 4
Peel down: 0.01 seconds
Peel up: 0.02 seconds
Core peeling cycles: 6.24 seconds
Heuristic Peeling: 7.34 seconds