R Under development (unstable) (2025-12-11 r89152 ucrt) -- "Unsuffered Consequences" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(AGHmatrix) > > test_check("AGHmatrix") Verifying conflicting data... Organizing data... Constructing matrix A using ploidy = 2 Completed! Time = 0 minutes Your data was chronologically organized with success. Verifying conflicting data... Organizing data... Constructing matrix A using ploidy = 2 Constructing dominance relationship matrix Completed! Time = 0.0001666667 minutes Your data was chronologically organized with success. Verifying conflicting data... Organizing data... Constructing matrix A using ploidy = 2 Completed! Time = 0 minutes Your data was chronologically organized with success. Verifying conflicting data... Organizing data... Constructing matrix A using ploidy = 4 and proportion of double reduction = 0 ;as in Kerr et al. (2012) Completed! Time = 0 minutes Your data was chronologically organized with success. Verifying conflicting data... Organizing data... Constructing matrix A using ploidy = 4 and proportion of double reduction = 0.1 ;as in Kerr et al. (2012) Completed! Time = 0 minutes Your data was chronologically organized with success. Verifying conflicting data... Organizing data... Constructing matrix A using ploidy = 4 and proportion of double reduction = 0.1 ;as in Slater et al. (2014) Completed! Time = 0 minutes Your data was chronologically organized with success. Verifying conflicting data... Organizing data... Constructing matrix A using ploidy = 6 and proportion of double reduction = 0 ;as in Kerr et al. (2012) Completed! Time = 0 minutes Your data was chronologically organized with success. Verifying conflicting data... Organizing data... Constructing matrix A using ploidy = 6 and proportion of double reduction = 0.05 ;as in Kerr et al. (2012) Completed! Time = 0 minutes Your data was chronologically organized with success. Verifying conflicting data... Organizing data... Constructing matrix A using ploidy = 2 Completed! Time = 0 minutes Your data was chronologically organized with success. Your data was not chronologically organized with success. Your data was not chronologically organized with success. Your data was not chronologically organized with success. Your data was not chronologically organized with success. Your data was not chronologically organized with success. Your data was chronologically organized with success. Missing data check: Total SNPs: 3 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3 SNPs Final: 3 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 3 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3 SNPs Final: 3 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 3 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3 SNPs Final: 3 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 3 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3 SNPs Final: 3 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 3 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3 SNPs Final: 3 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 0.5 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 0.5 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 6 0 SNPs dropped due to missing data threshold of 1 Total of: 6 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 6 SNPs Final: 6 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 4828 SNPs ( 25 SNPs removed) Missing data check: Total SNPs: 4853 0 SNPs dropped due to missing data threshold of 0.5 Total of: 4853 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 4853 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 4828 SNPs ( 25 SNPs removed) Missing data check: Total SNPs: 4853 0 SNPs dropped due to missing data threshold of 0.5 Total of: 4853 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 4853 SNPs ( 0 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: 1638 SNPs dropped with MAF below 0.05 Total: 3190 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3190 SNPs ( 1663 SNPs removed) Missing data check: Total SNPs: 4853 0 SNPs dropped due to missing data threshold of 0.5 Total of: 4853 SNPs MAF check: 1402 SNPs dropped with MAF below 0.05 Total: 3451 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3451 SNPs ( 1402 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: 1638 SNPs dropped with MAF below 0.05 Total: 3190 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3190 SNPs ( 1663 SNPs removed) Missing data check: Total SNPs: 4853 0 SNPs dropped due to missing data threshold of 0.5 Total of: 4853 SNPs MAF check: 1402 SNPs dropped with MAF below 0.05 Total: 3451 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3451 SNPs ( 1402 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: 1638 SNPs dropped with MAF below 0.05 Total: 3190 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3190 SNPs ( 1663 SNPs removed) Missing data check: Total SNPs: 4853 0 SNPs dropped due to missing data threshold of 0.5 Total of: 4853 SNPs MAF check: 1402 SNPs dropped with MAF below 0.05 Total: 3451 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3451 SNPs ( 1402 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: 1638 SNPs dropped with MAF below 0.05 Total: 3190 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3190 SNPs ( 1663 SNPs removed) Missing data check: Total SNPs: 4853 0 SNPs dropped due to missing data threshold of 0.5 Total of: 4853 SNPs MAF check: 1402 SNPs dropped with MAF below 0.05 Total: 3451 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3451 SNPs ( 1402 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: 1638 SNPs dropped with MAF below 0.05 Total: 3190 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3190 SNPs ( 1663 SNPs removed) Missing data check: Total SNPs: 4853 0 SNPs dropped due to missing data threshold of 0.5 Total of: 4853 SNPs MAF check: 1402 SNPs dropped with MAF below 0.05 Total: 3451 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3451 SNPs ( 1402 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: 1638 SNPs dropped with MAF below 0.05 Total: 3190 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3190 SNPs ( 1663 SNPs removed) Missing data check: Total SNPs: 4853 0 SNPs dropped due to missing data threshold of 0.5 Total of: 4853 SNPs MAF check: 1402 SNPs dropped with MAF below 0.05 Total: 3451 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3451 SNPs ( 1402 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: 1638 SNPs dropped with MAF below 0.05 Total: 3190 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3190 SNPs ( 1663 SNPs removed) Missing data check: Total SNPs: 4853 0 SNPs dropped due to missing data threshold of 0.5 Total of: 4853 SNPs MAF check: 1402 SNPs dropped with MAF below 0.05 Total: 3451 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3451 SNPs ( 1402 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: 1638 SNPs dropped with MAF below 0.05 Total: 3190 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3190 SNPs ( 1663 SNPs removed) Missing data check: Total SNPs: 4853 0 SNPs dropped due to missing data threshold of 0.5 Total of: 4853 SNPs MAF check: 1402 SNPs dropped with MAF below 0.05 Total: 3451 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3451 SNPs ( 1402 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 3895 0 SNPs dropped due to missing data threshold of 0.5 Total of: 3895 SNPs MAF check: 136 SNPs dropped with MAF below 0.05 Total: 3759 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 3895 SNPs Final: 3759 SNPs ( 136 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: 1638 SNPs dropped with MAF below 0.05 Total: 3190 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3190 SNPs ( 1663 SNPs removed) Missing data check: Total SNPs: 4853 25 SNPs dropped due to missing data threshold of 0.5 Total of: 4828 SNPs MAF check: 1638 SNPs dropped with MAF below 0.05 Total: 3190 SNPs Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 4853 SNPs Final: 3190 SNPs ( 1663 SNPs removed) Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0 minutes Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0.003666667 minutes Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0 minutes Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0 minutes Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0 minutes Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0 minutes Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0 minutes Returning H = A matrix corrected by G... Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Missing data check: Total SNPs: 8 0 SNPs dropped due to missing data threshold of 0.5 Total of: 8 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 8 SNPs Final: 8 SNPs ( 0 SNPs removed) Completed! Time = 0.001166667 minutes Returning H = A matrix corrected by G... Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0 minutes Returning H = A matrix corrected by G... Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Missing data check: Total SNPs: 5 0 SNPs dropped due to missing data threshold of 0.5 Total of: 5 SNPs MAF check: No SNPs with MAF below 0 Heterozigosity data check: No SNPs with heterozygosity, missing threshold of = 0 Summary check: Initial: 5 SNPs Final: 5 SNPs ( 0 SNPs removed) Completed! Time = 0 minutes Returning H = A matrix corrected by G... Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0 minutes Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0 minutes Comparing the matrices... Completed! Time = 0 minutes Computing the H matrix... Completed! Time = 0 minutes [ FAIL 0 | WARN 0 | SKIP 0 | PASS 193 ] > > proc.time() user system elapsed 227.00 39.42 266.40