Print basic info per generation
base_report_callback( userdir = "", generation, pop_pool, pareto, prob_matrix, current_time )
| userdir | the default directory used by `galgo()` to store files |
|---|---|
| generation | a number indicating the number of iterations of the galgo algorithm |
| pop_pool | a |
| pareto | the solutions found by Galgo across all generations in the solution space |
| prob_matrix | a |
| current_time | an |
#> Warning: object 'transbig' not foundexpression <- Biobase::exprs(Train) clinical <- Biobase::pData(Train) OS <- survival::Surv(time = clinical$t.rfs, event = clinical$e.rfs) # We will use a reduced dataset for the example expression <- expression[sample(1:nrow(expression), 100), ] # Now we scale the expression matrix expression <- t(scale(t(expression))) # Run galgo with base_report_callback assigned to the report_callback # hook-point galgoR::galgo(generations = 5, population = 15, prob_matrix = expression, OS = OS, report_callback = base_report_callback )#>#>#> k rnkIndex CrowD #> result.7 2 0.10888047 14.49866 1 Inf #> result.9 5 0.05056947 185.49095 1 0.7214049 #> result.10 2 0.06498447 160.66696 1 1.3679277 #> result.14 7 0.02128337 224.89984 1 Inf#>#> k rnkIndex CrowD #> result.7 2 0.10888047 14.49866 1 Inf #> result.14 7 0.02128337 224.89984 1 Inf #> result.9 5 0.05056947 185.49095 1 0.7175245 #> result.13 2 0.09296446 76.69576 1 0.6351903 #> result.8 2 0.07819196 87.59060 1 0.6134396 #> result.9 3 0.06559908 151.89572 1 0.4686648 #> result.10 2 0.06498447 160.66696 1 0.3007531#>#> k rnkIndex CrowD #> result.7 2 0.10888047 14.49866 1 Inf #> 10 0.00939784 294.48435 1 Inf #> 7 0.02889464 237.78186 1 0.6442515 #> result.13 2 0.09296446 76.69576 1 0.5460982 #> result.8 2 0.07819196 87.59060 1 0.5224424 #> 5 0.03951537 192.15347 1 0.3880625 #> result.9 3 0.06559908 151.89572 1 0.3823506 #> result.9 5 0.05056947 185.49095 1 0.3499488 #> result.10 2 0.06498447 160.66696 1 0.2596578#>#> k rnkIndex CrowD #> result.7 2 0.10888047 14.49866 1 Inf #> 10 0.00939784 294.48435 1 Inf #> 7 0.02889464 237.78186 1 0.6193555 #> 2 0.08554100 132.75042 1 0.4358089 #> 2 0.10800606 61.41323 1 0.3975359 #> 5 0.03951537 192.15347 1 0.3731564 #> result.9 5 0.05056947 185.49095 1 0.3366572 #> result.9 3 0.06559908 151.89572 1 0.2802297 #> 2 0.09556422 96.13645 1 0.2540836 #> result.10 2 0.06498447 160.66696 1 0.2496973 #> 2 0.09516738 102.11118 1 0.2148175#>#> k rnkIndex CrowD #> result.7 2 0.10888047 14.49866 1 Inf #> 10 0.00939784 294.48435 1 Inf #> 7 0.02889464 237.78186 1 0.6231472 #> 2 0.08554100 132.75042 1 0.4385594 #> 2 0.10800606 61.41323 1 0.3999103 #> 5 0.03951537 192.15347 1 0.3754756 #> result.9 5 0.05056947 185.49095 1 0.3388079 #> result.9 3 0.06559908 151.89572 1 0.2820135 #> 2 0.09556422 96.13645 1 0.2556438 #> result.10 2 0.06498447 160.66696 1 0.2512543 #> 2 0.09516738 102.11118 1 0.2161284#> An object of class "galgo.Obj" #> Slot "Solutions": #> 205766_at 38241_at 207078_at 210843_s_at 200957_s_at 219627_at #> result.7 0 0 1 0 0 1 #> 1 1 0 1 1 1 #> 0 0 1 0 0 1 #> 1 0 0 0 1 1 #> 0 0 0 0 0 1 #> 1 1 1 1 1 1 #> result.9 1 0 0 0 1 0 #> result.9 1 1 1 1 1 1 #> 0 0 1 1 1 1 #> result.10 1 1 1 1 1 1 #> 0 0 1 0 0 1 #> result.13 1 0 1 1 1 1 #> 1 1 0 1 1 1 #> 1 1 0 1 1 1 #> 1 1 1 1 1 1 #> 215890_at 218495_at 212079_s_at 202717_s_at 221636_s_at 213443_at #> result.7 0 1 0 0 0 0 #> 0 0 1 1 1 1 #> 0 1 1 0 0 0 #> 0 0 0 1 1 0 #> 0 1 0 0 0 0 #> 1 1 1 1 1 1 #> result.9 0 0 0 0 0 0 #> result.9 1 1 1 1 1 1 #> 0 1 0 0 1 0 #> result.10 1 1 1 1 1 1 #> 0 1 0 0 0 0 #> result.13 0 1 0 0 1 0 #> 0 0 1 1 1 1 #> 0 0 1 1 1 1 #> 0 1 1 1 1 1 #> 204646_at 219635_at 212306_at 216050_at 213462_at 216458_at 203845_at #> result.7 0 1 0 0 0 1 1 #> 1 1 1 1 1 1 1 #> 0 0 1 0 0 1 0 #> 0 1 1 0 1 1 0 #> 0 1 0 0 0 1 1 #> 1 1 1 1 1 1 1 #> result.9 0 1 1 0 1 1 0 #> result.9 1 1 1 1 1 1 1 #> 0 1 0 0 0 1 1 #> result.10 1 1 1 1 1 1 1 #> 0 1 0 0 0 1 1 #> result.13 0 1 0 1 0 1 1 #> 1 1 1 1 1 1 1 #> 1 1 1 1 1 1 1 #> 0 1 1 1 0 1 1 #> 202453_s_at 213453_x_at 212975_at 202519_at 215409_at 220352_x_at #> result.7 0 0 0 0 1 0 #> 1 0 1 0 1 1 #> 1 1 0 1 1 1 #> 0 0 0 0 0 1 #> 0 0 0 0 1 1 #> 1 1 0 1 1 1 #> result.9 0 0 0 0 0 1 #> result.9 0 1 1 0 1 1 #> 0 1 0 0 1 1 #> result.10 1 1 1 1 1 1 #> 0 0 0 0 1 0 #> result.13 0 1 0 0 1 1 #> 1 0 1 0 1 1 #> 1 0 1 0 1 1 #> 0 1 1 1 1 1 #> 209451_at 214150_x_at 212434_at 214840_at 212423_at 209798_at #> result.7 0 0 0 0 1 0 #> 0 0 1 0 0 0 #> 1 0 1 1 1 0 #> 1 0 1 0 1 0 #> 0 0 0 0 1 0 #> 0 1 1 1 1 1 #> result.9 1 1 0 1 1 0 #> result.9 1 1 1 0 1 0 #> 0 0 0 0 1 0 #> result.10 0 1 1 1 1 1 #> 0 0 0 0 1 0 #> result.13 0 0 0 0 1 0 #> 0 0 1 0 0 0 #> 0 0 1 0 0 0 #> 1 1 1 1 1 0 #> 211061_s_at 206768_at 218042_at 218309_at 221297_at 212062_at #> result.7 0 0 0 0 0 1 #> 1 1 1 1 1 1 #> 1 1 0 0 1 0 #> 0 0 1 0 1 1 #> 1 0 0 0 0 1 #> 0 1 1 1 1 1 #> result.9 0 0 0 0 1 1 #> result.9 1 1 1 1 1 1 #> 1 0 1 0 1 1 #> result.10 1 1 1 1 1 1 #> 0 0 0 0 0 1 #> result.13 1 0 1 0 1 1 #> 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> 1 1 1 1 1 0 #> 202542_s_at 218941_at 214003_x_at 214608_s_at 204748_at 221953_s_at #> result.7 1 0 0 0 0 0 #> 1 0 1 1 0 0 #> 0 1 0 1 1 0 #> 0 0 0 1 1 0 #> 1 0 0 0 0 0 #> 1 1 1 1 0 0 #> result.9 0 0 0 1 1 0 #> result.9 1 1 1 1 1 0 #> 1 0 0 1 0 0 #> result.10 1 1 1 1 1 0 #> 1 0 0 0 0 0 #> result.13 1 0 0 1 0 0 #> 1 0 1 1 0 0 #> 1 0 1 1 0 0 #> 1 1 1 1 1 0 #> 218580_x_at 205064_at 44563_at 206783_at 213170_at 203257_s_at #> result.7 0 0 0 0 0 0 #> 1 0 1 0 1 1 #> 0 1 0 0 1 1 #> 0 0 1 1 1 1 #> 0 0 0 0 0 0 #> 1 1 1 1 1 1 #> result.9 0 0 1 1 1 0 #> result.9 1 1 1 1 1 1 #> 0 0 1 0 0 0 #> result.10 1 1 1 1 1 1 #> 0 0 0 0 0 0 #> result.13 0 0 1 0 0 0 #> 1 0 1 0 1 1 #> 1 0 1 0 1 1 #> 0 1 1 1 1 1 #> 203397_s_at 218895_at 202312_s_at 201787_at 204400_at 202302_s_at #> result.7 0 1 1 0 0 0 #> 1 1 1 1 0 1 #> 1 0 0 0 1 1 #> 1 0 0 0 1 0 #> 0 1 1 0 0 0 #> 1 1 1 1 1 1 #> result.9 1 0 0 0 1 0 #> result.9 1 1 1 1 1 1 #> 0 1 1 0 0 0 #> result.10 1 1 1 1 1 1 #> 0 1 1 0 0 0 #> result.13 0 1 1 0 0 1 #> 1 1 1 1 0 1 #> 1 1 1 1 0 1 #> 1 1 1 0 1 1 #> 207070_at 217765_at 219645_at 214593_at 211868_x_at 204315_s_at #> result.7 0 0 0 0 1 0 #> 0 0 1 0 1 1 #> 0 0 0 0 1 1 #> 0 1 0 0 1 1 #> 0 0 0 0 1 0 #> 1 1 0 1 1 1 #> result.9 0 1 0 0 1 0 #> result.9 1 0 1 0 1 1 #> 0 0 0 0 0 1 #> result.10 1 1 1 1 1 1 #> 0 0 0 0 1 0 #> result.13 0 0 0 0 0 1 #> 0 0 1 0 1 1 #> 0 0 1 0 1 1 #> 1 0 1 0 1 1 #> 210288_at 201689_s_at 214930_at 216444_at 203557_s_at 39835_at #> result.7 0 1 0 1 0 0 #> 1 1 1 1 1 1 #> 1 1 1 1 1 0 #> 0 0 0 0 1 0 #> 0 1 0 1 0 0 #> 1 1 1 1 1 1 #> result.9 0 0 0 0 1 0 #> result.9 1 1 1 1 1 1 #> 1 1 0 1 0 0 #> result.10 1 1 1 1 1 1 #> 0 1 0 1 0 0 #> result.13 1 1 0 1 1 0 #> 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> 202305_s_at 220670_at 221219_s_at 214941_s_at 211665_s_at 200974_at #> result.7 1 0 0 0 0 0 #> 1 1 0 1 1 1 #> 0 1 0 0 1 1 #> 1 1 1 1 0 1 #> 1 1 0 1 0 0 #> 1 1 1 1 1 1 #> result.9 1 1 1 1 0 1 #> result.9 1 1 1 1 1 1 #> 1 0 1 0 0 0 #> result.10 1 1 1 1 1 1 #> 1 0 0 0 0 0 #> result.13 1 0 1 0 0 0 #> 1 1 0 1 1 1 #> 1 1 0 1 1 1 #> 1 1 1 1 1 1 #> 211066_x_at 201245_s_at 42361_g_at 214304_x_at 201225_s_at 1494_f_at #> result.7 1 1 0 1 0 0 #> 0 1 1 1 1 1 #> 0 1 0 1 0 1 #> 0 0 1 1 1 0 #> 1 1 0 1 0 0 #> 1 1 1 0 1 1 #> result.9 0 0 1 0 0 0 #> result.9 1 1 1 1 1 1 #> 1 1 0 1 1 1 #> result.10 1 1 1 1 1 1 #> 1 1 0 1 0 0 #> result.13 1 1 0 1 1 1 #> 0 1 1 1 1 1 #> 0 1 1 1 1 1 #> 1 1 1 1 1 1 #> 218653_at 206010_at 209287_s_at 204857_at 217214_s_at 216919_at #> result.7 0 0 1 1 0 0 #> 1 0 1 0 1 0 #> 0 0 0 1 1 0 #> 1 0 1 0 1 0 #> 0 0 1 1 0 0 #> 1 1 1 1 1 1 #> result.9 1 0 1 0 1 0 #> result.9 1 1 1 1 1 0 #> 1 0 1 1 1 0 #> result.10 1 1 1 1 1 1 #> 0 0 1 1 0 0 #> result.13 1 0 1 1 1 0 #> 1 0 1 0 1 0 #> 1 0 1 0 1 0 #> 1 0 1 1 1 0 #> 218306_s_at 208328_s_at 213379_at 211370_s_at 211263_s_at 203906_at #> result.7 0 0 0 0 1 0 #> 1 1 1 1 1 0 #> 1 1 0 1 1 1 #> 0 1 1 1 0 0 #> 1 0 0 0 1 0 #> 1 1 1 1 1 0 #> result.9 0 0 0 1 0 1 #> result.9 1 0 1 1 1 0 #> 0 0 1 1 1 0 #> result.10 1 1 1 1 1 1 #> 0 0 0 0 1 0 #> result.13 1 0 1 1 1 0 #> 1 1 1 1 1 0 #> 1 1 1 1 1 0 #> 1 0 1 1 1 0 #> 205524_s_at 212900_at 216668_at 203398_s_at 205106_at 207812_s_at #> result.7 0 0 0 0 0 0 #> 1 1 0 1 1 1 #> 0 1 1 0 1 0 #> 0 1 1 1 1 0 #> 0 0 0 1 0 0 #> 1 1 1 1 0 1 #> result.9 0 1 1 1 1 0 #> result.9 0 1 1 1 1 1 #> 0 1 1 1 1 0 #> result.10 1 1 1 1 1 1 #> 0 0 0 0 0 0 #> result.13 0 1 1 1 1 0 #> 1 1 0 1 1 1 #> 1 1 0 1 1 1 #> 0 1 1 1 1 1 #> 211921_x_at 202926_at 206606_at k rnkIndex #> result.7 0 1 0 2 0.108880468 14.49866 1 #> 1 1 0 10 0.009397840 294.48435 1 #> 0 1 1 7 0.028894640 237.78186 1 #> 0 0 1 2 0.085541004 132.75042 1 #> 0 1 0 2 0.108006062 61.41323 1 #> 1 1 1 5 0.039515369 192.15347 1 #> result.9 0 0 1 5 0.050569465 185.49095 1 #> result.9 1 0 1 3 0.065599078 151.89572 1 #> 0 1 0 2 0.095564224 96.13645 1 #> result.10 1 1 1 2 0.064984472 160.66696 1 #> 0 1 0 2 0.095167382 102.11118 1 #> result.13 0 1 0 2 0.092964459 76.69576 2 #> 1 1 0 10 -0.001285935 250.12797 2 #> 1 1 0 10 -0.001285935 250.12797 2 #> 1 0 1 4 0.051347347 138.06628 2 #> CrowD #> result.7 Inf #> Inf #> 0.6231472 #> 0.4385594 #> 0.3999103 #> 0.3754756 #> result.9 0.3388079 #> result.9 0.2820135 #> 0.2556438 #> result.10 0.2512543 #> 0.2161284 #> result.13 Inf #> Inf #> Inf #> 0.7055311 #> #> Slot "ParetoFront": #> [[1]] #> [,1] [,2] #> result.1 0.029072714 59.57509 #> result.2 0.026890329 100.89280 #> result.3 0.003859345 76.48396 #> result.4 0.027466504 20.62048 #> result.5 0.019864753 47.13439 #> result.6 0.025348479 27.85536 #> result.7 0.108880468 14.49866 #> result.8 0.006243922 195.69724 #> result.9 0.050569465 185.49095 #> result.10 0.064984472 160.66696 #> result.11 0.050805401 35.34028 #> result.12 0.004287988 119.05332 #> result.13 0.051706671 48.16061 #> result.14 0.021283369 224.89984 #> #> [[2]] #> #> result.7 0.108880468 14.49866 #> result.14 0.021283369 224.89984 #> result.9 0.050569465 185.49095 #> result.13 0.092964459 76.69576 #> result.8 0.078191962 87.59060 #> result.9 0.065599078 151.89572 #> result.10 0.064984472 160.66696 #> result.2 0.073458271 65.89272 #> result.14 0.006159749 198.78661 #> result.15 0.063970858 115.59789 #> result.6 0.024414391 181.19219 #> result.8 0.006243922 195.69724 #> result.12 0.004287988 119.05332 #> result.13 0.051706671 48.16061 #> result.1 0.046506341 100.24508 #> #> [[3]] #> #> result.7 0.108880468 14.49866 #> 0.009397840 294.48435 #> 0.028894640 237.78186 #> result.13 0.092964459 76.69576 #> result.8 0.078191962 87.59060 #> 0.039515369 192.15347 #> result.9 0.065599078 151.89572 #> result.9 0.050569465 185.49095 #> result.10 0.064984472 160.66696 #> 0.002088606 246.68491 #> 0.075645449 59.48730 #> 0.051347347 138.06628 #> result.6 0.024414391 181.19219 #> result.15 0.063970858 115.59789 #> 0.023759291 230.56073 #> #> [[4]] #> #> result.7 0.108880468 14.49866 #> 0.009397840 294.48435 #> 0.028894640 237.78186 #> 0.085541004 132.75042 #> 0.108006062 61.41323 #> 0.039515369 192.15347 #> result.9 0.050569465 185.49095 #> result.9 0.065599078 151.89572 #> 0.095564224 96.13645 #> result.10 0.064984472 160.66696 #> 0.095167382 102.11118 #> result.13 0.092964459 76.69576 #> 0.002088606 246.68491 #> 0.051347347 138.06628 #> result.6 0.024414391 181.19219 #> #> [[5]] #> #> result.7 0.108880468 14.49866 #> 0.009397840 294.48435 #> 0.028894640 237.78186 #> 0.085541004 132.75042 #> 0.108006062 61.41323 #> 0.039515369 192.15347 #> result.9 0.050569465 185.49095 #> result.9 0.065599078 151.89572 #> 0.095564224 96.13645 #> result.10 0.064984472 160.66696 #> 0.095167382 102.11118 #> result.13 0.092964459 76.69576 #> -0.001285935 250.12797 #> -0.001285935 250.12797 #> 0.051347347 138.06628 #> #>