CBLUP90IOD CBLUP90IOD is a threshold-linear program for obtaining solutions to very large models. Solutions are obtained by iteration on data using the preconditioned conjugate iteration. History - Original linear model program BLUPF90 (I. Misztal) - Rewrite to threshold-linear model program CBLUP90 (I. Misztal) - Rewrite to multiple linear traits with computed thresholds and multiple linear traits(B. Auvray) - Rewrite of BLUPF90 to iteration on data: BLUP90IOD (S. Tsuruta) CBLUP90IOD supports models with one categorical trait and multiple linear traits. Thresholds are computed but none of the variances is. Memory requirements are about 56 bytes per equation. These requirements would be halved if large variables are converted to single-precision, however, such a modification has not been tested. For details on how to construct te parameter files, see the documentation on BLUPF90. For details specific to threshold models, see the documentation on CBLUP90 and CBLUP90THR. Copyrighted by Ignacy Misztal (ignacy@uga.edu) and the University of Georgia. Last modified 10/11/19990 Available options: OPTION conv_crit 1d-12 Convergence criterion (default 1d-12). OPTION maxrounds 500 Maximum rounds (default 5000). OPTION cont Keep the last solutions and residuals for restart. OPTION cont 1 Restart the program from the last run using the previous solutions. OPTION category 3 Number of category (default 4) Example 1 ---------- [ignacy@dodo2]$ cat ex1.par DATAFILE ex1.dat NUMBER_OF_TRAITS NUMBER_OF_EFFECTS OBSERVATION(S) 16 14 15 WEIGHT(S) EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] 1 1 1 53 cross 5 5 5 2 cross 6 6 6 1 cross 10 0 10 1 cross RANDOM_RESIDUAL VALUES 1 15 3 15 726 29.8509 3 29.8509 22.078 RANDOM_GROUP RANDOM_TYPE add_animal FILE ex1.ped (CO)VARIANCES 0.42857 -7.202 .6462 -7.202 484 15.198 .6462 15.198 3.9 [ignacy@dodo2]$ cat ex1.dat 53 6 0 7 2 1 0 6 1 0 10 1 0 290.0 36.5 1 52 6 0 7 2 1 0 6 1 0 10 1 0 317.8 43.5 2 51 6 0 7 1 0 0 5 0 0 9 0 0 256.5 36.0 1 50 6 0 7 1 0 0 5 0 1 9 0 1 315.0 45.0 1 49 6 0 7 1 0 0 5 0 1 9 0 1 273.0 46.0 2 48 6 0 7 1 0 0 5 0 1 9 0 1 354.8 50.5 3 47 6 0 7 1 1 0 5 1 0 9 1 0 357.0 36.5 1 46 6 0 7 1 1 0 5 1 1 9 1 1 260.0 45.3 2 45 6 0 7 1 1 0 5 1 0 9 1 0 290.0 51.6 3 44 5 0 7 2 0 0 6 0 1 10 0 1 346.5 51.0 2 43 5 0 7 2 0 0 6 0 1 10 0 1 317.8 43.7 2 42 5 0 7 2 1 0 6 1 1 10 1 1 357.0 50.5 2 41 5 0 7 2 1 0 6 1 0 10 1 0 357.0 41.0 1 40 5 0 7 1 0 0 5 0 0 9 0 0 344.0 48.0 3 39 5 0 7 1 0 0 5 0 1 9 0 1 346.5 52.0 1 38 5 0 7 1 0 0 5 0 1 9 0 1 328.0 38.5 1 37 5 0 7 1 0 0 5 0 1 9 0 1 285.0 48.8 2 36 5 0 7 1 0 0 5 0 1 9 0 1 396.0 42.5 1 35 5 0 7 1 1 0 5 1 0 9 1 0 304.5 43.5 1 34 5 0 7 1 1 0 5 1 1 9 1 1 346.5 40.5 1 33 4 0 7 2 1 0 6 1 1 10 1 1 333.3 44.5 1 32 4 0 7 1 0 0 5 0 0 9 0 0 243.0 39.0 1 31 4 0 7 1 0 0 5 0 0 9 0 0 344.0 51.0 2 30 4 0 7 1 0 0 5 0 1 9 0 1 328.0 47.0 2 29 3 0 7 2 0 0 6 0 1 10 0 1 320.0 46.0 1 28 3 0 7 2 0 0 6 0 0 10 0 0 302.3 44.4 1 27 3 0 7 2 0 0 6 0 0 10 0 0 266.0 32.5 1 26 3 0 7 2 1 0 6 1 0 10 1 0 328.0 42.7 1 25 3 0 7 2 1 0 6 1 1 10 1 1 300.0 36.0 1 24 3 0 7 1 1 0 5 1 1 9 1 1 341.0 41.6 1 23 2 0 7 2 0 0 6 0 1 10 0 1 273.0 49.0 1 22 2 0 7 2 0 0 6 0 1 10 0 1 300.0 44.5 1 21 2 0 7 1 0 0 5 0 1 9 0 1 315.0 42.0 1 20 2 0 7 1 0 0 5 0 1 9 0 1 307.5 47.0 2 19 2 0 7 1 0 0 5 0 0 9 0 0 346.5 34.0 1 18 2 0 7 1 1 0 5 1 1 9 1 1 333.3 43.0 2 17 2 0 7 1 1 0 5 1 1 9 1 1 346.5 41.4 1 16 1 0 7 2 0 0 6 0 0 10 0 0 346.5 39.0 1 15 1 0 7 2 1 0 6 1 0 10 1 0 374.0 40.5 1 14 1 0 7 2 1 0 6 1 0 10 1 0 336.0 46.0 1 13 1 0 7 1 0 0 5 0 0 9 0 0 270.0 35.0 1 12 1 0 7 1 0 0 5 0 0 9 0 0 310.0 42.0 1 11 1 0 7 1 0 0 5 0 0 9 0 0 285.0 43.0 1 10 1 0 7 1 0 0 5 0 0 9 0 0 374.0 40.0 1 9 1 0 7 1 1 0 5 1 0 9 1 0 354.8 41.5 1 8 1 0 7 1 1 0 5 1 1 9 1 1 304.5 37.5 1 7 1 0 7 1 1 0 5 1 1 9 1 1 328.0 41.0 1 [ignacy@dodo2]$ cat ex1.ped 53 6 0 52 6 0 51 6 0 50 6 0 49 6 0 48 6 0 47 6 0 46 6 0 45 6 0 44 5 0 43 5 0 42 5 0 41 5 0 40 5 0 39 5 0 38 5 0 37 5 0 36 5 0 35 5 0 34 5 0 33 4 0 32 4 0 31 4 0 30 4 0 29 3 0 28 3 0 27 3 0 26 3 0 25 3 0 24 3 0 23 2 0 22 2 0 21 2 0 20 2 0 19 2 0 18 2 0 17 2 0 16 1 0 15 1 0 14 1 0 13 1 0 12 1 0 11 1 0 10 1 0 9 1 0 8 1 0 7 1 0 6 0 0 5 0 0 4 0 0 3 0 0 2 0 0 1 0 0 [ignacy@dodo2]$ cblup90iod number of categories (numbered from 1)? name of parameter file?ex1.par CBLUP90IOD 1.0 by I. Misztal, 10/11/99 Parameter file: ex1.par Data file: ex1.dat Number of Traits 3 Number of Effects 4 Position of Observations 16 14 15 Position of Weight (1) 0 Value of Missing Trait/Observation 0 EFFECTS # type position (2) levels [positions for nested] 1 cross-classified 1 1 1 53 2 cross-classified 5 5 5 2 3 cross-classified 6 6 6 1 4 cross-classified 10 0 10 1 Residual (co)variance Matrix 1.0000 15.000 3.0000 15.000 726.00 29.851 3.0000 29.851 22.078 Random Effect(s) 1 Type of Random Effect: additive animal Pedigree File: ex1.ped trait effect (CO)VARIANCES 1 1 0.42857 -7.2020 0.64620 2 1 -7.2020 484.00 15.198 3 1 0.64620 15.198 3.9000 REMARKS (1) Weight position 0 means no weights utilized (2) Effect positions of 0 for some effects and traits means that such effects are missing for specified traits Data record length = 16 number of rounds? initial thresholds: -0.5000 -0.0000 0.42857 -7.2020 0.64620 -7.2020 484.00 15.198 0.64620 15.198 3.9000 G inverse 10.094 0.23098 -2.5726 0.23098 0.76397E-02 -0.68043E-01 -2.5726 -0.68043E-01 0.94782 read 47 records eps = 1.545122445227030E-011 no. of iteration = 49 thresholds in round 1: -0.47537 0.00000 eps = 2.114189614579900E-011 no. of iteration = 46 thresholds in round 2: -0.99853 0.00000 eps = 3.195444694991311E-011 no. of iteration = 44 thresholds in round 3: -1.21192 0.00000 eps = 4.229633202398320E-011 no. of iteration = 44 thresholds in round 4: -1.26689 0.00000 solutions stored in file: "solutions" Example 2 ---------- [ignacy@dodo2]$ cat ex2.par # Large simulated data set # 3 traits, first one categorical (4 categories). DATAFILE ex2.dat NUMBER_OF_TRAITS NUMBER_OF_EFFECTS OBSERVATION(S) 3 4 5 WEIGHT(S) EFFECTS: POSITIONS_IN_DATAFILE NUMBER_OF_LEVELS TYPE_OF_EFFECT [EFFECT NESTED] 2 2 2 50 cross 1 1 1 1100 cross RANDOM_RESIDUAL VALUES 1.0000 7.7460 7.7460 7.7460 1351.0 231.81 7.7460 231.81 1369.0 RANDOM_GROUP RANDOM_TYPE add_animal FILE ex2.ped (CO)VARIANCES 0.66667 5.16398 5.16398 5.16398 1000.00000 200.00000 5.16398 200.00000 1000.00000 [ignacy@dodo2]$ icblup90iod number of categories (numbered from 1)? name of parameter file?ex2.par CBLUP90IOD 1.0 by I. Misztal, 10/11/99 Parameter file: ex2.par Data file: ex2.dat Number of Traits 3 Number of Effects 2 Position of Observations 3 4 5 Position of Weight (1) 0 Value of Missing Trait/Observation 0 EFFECTS # type position (2) levels [positions for nested] 1 cross-classified 2 2 2 50 2 cross-classified 1 1 1 1100 Residual (co)variance Matrix 1.0000 7.7460 7.7460 7.7460 1351.0 231.81 7.7460 231.81 1369.0 Random Effect(s) 2 Type of Random Effect: additive animal Pedigree File: ex2.ped trait effect (CO)VARIANCES 1 2 0.66667 5.1640 5.1640 2 2 5.1640 1000.0 200.00 3 2 5.1640 200.00 1000.0 REMARKS (1) Weight position 0 means no weights utilized (2) Effect positions of 0 for some effects and traits means that such effects are missing for specified traits Data record length = 5 number of rounds? initial thresholds: -0.6667 -0.3333 -0.0000 0.66667 5.1640 5.1640 5.1640 1000.0 200.00 5.1640 200.00 1000.0 G inverse 1.6071 -0.69160E-02 -0.69160E-02 -0.69160E-02 0.10714E-02 -0.17857E-03 -0.69160E-02 -0.17857E-03 0.10714E-02 read 1000 records eps = 9.400106129966520E-011 no. of iteration = 41 thresholds in round 1: -1.38764 -0.61188 0.00000 eps = 9.044560960701230E-011 no. of iteration = 44 thresholds in round 2: -1.86832 -0.90333 0.00000 eps = 5.262946997597152E-011 no. of iteration = 46 thresholds in round 3: -2.08856 -1.02189 0.00000 eps = 8.666286752404070E-011 no. of iteration = 46 thresholds in round 4: -2.15157 -1.05558 0.00000 eps = 9.584502638477410E-011 no. of iteration = 46 thresholds in round 5: -2.16738 -1.06370 0.00000 solutions stored in file: "solutions"