Print basic info per generation
callback_base_report (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 |
Nothing.
#> 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 GSgalgoR::galgo(generations = 5, population = 15, prob_matrix = expression, OS = OS, report_callback = callback_base_report )#>#>#> 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.10 2 0.09127924 97.48479 1 1.0479639 #> result.10 2 0.06498447 160.66696 1 0.7587684 #> result.9 5 0.05056947 185.49095 1 0.6560957 #> result.12 10 0.02257438 222.37007 1 0.4387219#>#> k rnkIndex CrowD #> result.7 2 0.10888047 14.49866 1 Inf #> 10 0.01637632 254.46413 1 Inf #> result.10 2 0.09127924 97.48479 1 0.9732332 #> result.10 2 0.06498447 160.66696 1 0.7145353 #> result.9 5 0.05056947 185.49095 1 0.6258221 #> result.12 10 0.02257438 222.37007 1 0.4195039 #> result.14 7 0.02128337 224.89984 1 0.1827214#>#> k rnkIndex CrowD #> result.7 2 0.10888047 14.49866 1 Inf #> 10 0.01637632 254.46413 1 Inf #> result.10 2 0.09127924 97.48479 1 0.9524847 #> result.10 2 0.06498447 160.66696 1 0.6964094 #> result.9 5 0.05056947 185.49095 1 0.6076431 #> result.12 10 0.02257438 222.37007 1 0.4070256 #> result.14 7 0.02128337 224.89984 1 0.1795228#>#> k rnkIndex CrowD #> result.7 2 0.10888047 14.49866 1 Inf #> 10 0.01637632 254.46413 1 Inf #> result.10 2 0.09127924 97.48479 1 0.9381609 #> result.10 2 0.06498447 160.66696 1 0.6797534 #> 7 0.04094213 227.00361 1 0.5511496 #> result.9 5 0.05056947 185.49095 1 0.4589268#> 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 #> result.10 0 0 1 0 0 1 #> result.10 1 1 1 1 1 1 #> 1 0 0 1 1 1 #> result.9 1 0 0 0 1 0 #> 0 0 1 0 0 1 #> 0 0 1 0 0 1 #> result.7 0 0 1 1 0 0 #> 1 0 1 1 1 1 #> 0 1 1 1 1 1 #> result.8 1 1 0 1 1 1 #> 1 1 1 1 1 1 #> result.14 0 0 1 0 0 1 #> result.12 0 1 0 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 #> 1 1 1 1 1 1 #> result.10 0 1 0 0 0 0 #> result.10 1 1 1 1 1 1 #> 1 0 0 0 0 1 #> result.9 0 0 0 0 0 0 #> 0 1 0 0 0 0 #> 0 1 0 0 0 0 #> result.7 0 0 0 0 1 0 #> 1 0 0 0 1 0 #> 0 1 1 1 0 1 #> result.8 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> result.14 0 0 1 1 0 0 #> result.12 1 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 #> result.10 0 1 0 0 0 1 1 #> result.10 1 1 1 1 1 1 1 #> 0 1 1 0 1 1 0 #> result.9 0 1 1 0 1 1 0 #> 0 1 0 0 0 1 1 #> 0 1 0 0 0 1 1 #> result.7 0 1 0 1 0 1 1 #> 0 1 0 0 0 1 1 #> 1 1 1 0 0 0 1 #> result.8 1 1 1 1 1 1 1 #> 1 1 1 1 1 1 1 #> result.14 1 1 1 0 1 1 0 #> result.12 1 1 1 1 1 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 1 1 0 1 1 #> result.10 0 0 0 0 1 0 #> result.10 1 1 1 1 1 1 #> 0 0 1 0 0 1 #> result.9 0 0 0 0 0 1 #> 0 0 0 0 1 0 #> 0 0 0 0 1 0 #> result.7 1 0 0 0 1 0 #> 1 1 1 0 1 1 #> 0 1 0 0 1 0 #> result.8 0 1 1 0 1 1 #> 1 1 1 1 1 1 #> result.14 1 1 0 1 1 1 #> result.12 0 1 1 0 1 1 #> 209451_at 214150_x_at 212434_at 214840_at 212423_at 209798_at #> result.7 0 0 0 0 1 0 #> 0 1 1 1 1 0 #> result.10 0 0 0 1 1 0 #> result.10 0 1 1 1 1 1 #> 1 1 0 1 1 0 #> result.9 1 1 0 1 1 0 #> 0 0 0 0 1 0 #> 0 0 0 1 1 0 #> result.7 0 1 0 0 1 0 #> 0 0 0 1 1 1 #> 0 1 1 1 1 1 #> result.8 0 1 1 0 1 0 #> 0 1 1 1 1 1 #> result.14 1 0 1 1 1 0 #> result.12 0 1 1 0 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 #> result.10 0 0 0 1 0 1 #> result.10 1 1 1 1 1 1 #> 0 0 1 0 1 1 #> result.9 0 0 0 0 1 1 #> 0 0 0 0 0 1 #> 0 0 0 1 0 1 #> result.7 0 0 0 0 0 1 #> 1 1 1 1 0 1 #> 1 0 1 0 0 1 #> result.8 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> result.14 1 1 1 1 1 0 #> result.12 0 1 1 1 1 1 #> 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 1 0 #> result.10 1 0 0 0 1 0 #> result.10 1 1 1 1 1 0 #> 0 0 0 1 1 0 #> result.9 0 0 0 1 1 0 #> 1 0 0 0 1 0 #> 1 0 0 0 1 0 #> result.7 1 0 0 0 0 1 #> 1 1 0 0 0 0 #> 1 0 0 1 1 1 #> result.8 1 0 1 1 1 0 #> 1 1 1 1 1 0 #> result.14 0 1 0 1 1 1 #> result.12 1 0 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 1 1 1 #> result.10 0 0 0 0 0 0 #> result.10 1 1 1 1 1 1 #> 0 0 1 1 1 0 #> result.9 0 0 1 1 1 0 #> 0 0 0 0 0 0 #> 0 0 0 0 0 0 #> result.7 0 1 0 0 0 0 #> 1 1 1 0 1 1 #> 0 0 0 0 0 1 #> result.8 1 0 1 1 1 1 #> 1 1 1 1 1 1 #> result.14 0 1 1 0 1 1 #> result.12 1 0 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 1 1 #> result.10 0 1 1 0 0 0 #> result.10 1 1 1 1 1 1 #> 1 0 0 1 1 1 #> result.9 1 0 0 0 1 0 #> 0 1 1 0 0 0 #> 0 1 1 0 0 0 #> result.7 0 0 0 0 1 0 #> 1 1 1 1 1 0 #> 0 1 1 0 1 1 #> result.8 1 1 1 0 1 1 #> 1 1 1 1 1 1 #> result.14 1 0 1 1 1 1 #> result.12 1 1 1 1 1 1 #> 207070_at 217765_at 219645_at 214593_at 211868_x_at 204315_s_at #> result.7 0 0 0 0 1 0 #> 1 0 1 0 0 1 #> result.10 0 0 0 0 0 0 #> result.10 1 1 1 1 1 1 #> 0 1 1 0 1 0 #> result.9 0 1 0 0 1 0 #> 0 0 0 0 1 0 #> 0 0 0 0 0 0 #> result.7 0 1 0 0 1 0 #> 1 1 0 0 1 1 #> 1 1 1 0 1 1 #> result.8 1 0 1 0 0 1 #> 1 1 1 1 1 1 #> result.14 0 1 0 0 0 1 #> result.12 1 0 1 0 0 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 #> result.10 0 1 0 1 0 0 #> result.10 1 1 1 1 1 1 #> 0 0 1 0 1 1 #> result.9 0 0 0 0 1 0 #> 0 1 0 1 0 0 #> 0 1 0 1 0 0 #> result.7 0 1 0 0 1 0 #> 1 1 1 1 0 1 #> 0 1 0 1 1 1 #> result.8 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> result.14 1 1 1 1 1 1 #> result.12 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 #> result.10 1 0 0 0 0 0 #> result.10 1 1 1 1 1 1 #> 1 1 1 1 0 1 #> result.9 1 1 1 1 0 1 #> 0 0 0 0 0 0 #> 1 0 0 0 0 0 #> result.7 1 1 0 0 0 0 #> 1 1 0 0 1 0 #> 1 0 1 1 0 1 #> result.8 1 1 0 1 1 1 #> 0 1 1 1 1 1 #> result.14 0 1 1 0 1 1 #> result.12 1 1 0 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 #> result.10 1 1 0 1 0 0 #> result.10 1 1 1 1 1 1 #> 0 0 1 0 1 1 #> result.9 0 0 1 0 0 0 #> 1 1 0 1 0 0 #> 1 1 0 1 0 0 #> result.7 1 1 0 0 1 0 #> 1 1 1 1 1 1 #> 1 1 0 1 1 0 #> result.8 1 1 1 1 1 1 #> 1 1 1 1 0 1 #> result.14 1 1 0 1 0 1 #> result.12 0 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 1 1 1 1 1 #> result.10 0 0 1 1 0 1 #> result.10 1 1 1 1 1 1 #> 1 0 1 1 1 0 #> result.9 1 0 1 0 1 0 #> 0 0 1 1 0 1 #> 0 0 1 1 0 1 #> result.7 0 0 1 0 0 0 #> 1 0 1 1 1 1 #> 0 0 1 1 0 1 #> result.8 1 1 1 1 1 0 #> 1 1 1 1 1 1 #> result.14 1 1 1 1 1 1 #> result.12 1 1 0 1 0 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 1 #> result.10 0 0 0 0 1 0 #> result.10 1 1 1 1 1 1 #> 0 0 0 1 0 1 #> result.9 0 0 0 1 0 1 #> 0 0 0 1 1 0 #> 0 0 0 0 1 0 #> result.7 0 0 0 1 1 0 #> 1 0 1 1 1 1 #> 0 0 1 1 1 1 #> result.8 1 1 1 1 1 0 #> 1 1 1 1 1 1 #> result.14 1 1 1 1 1 1 #> result.12 1 1 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 1 1 1 1 #> result.10 0 0 0 0 0 0 #> result.10 1 1 1 1 1 1 #> 0 1 1 1 1 1 #> result.9 0 1 1 1 1 0 #> 0 0 0 0 0 0 #> 0 0 0 0 0 0 #> result.7 0 0 0 0 0 0 #> 1 1 1 1 1 1 #> 0 0 1 0 1 1 #> result.8 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> result.14 0 1 1 1 1 1 #> result.12 1 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 1 10 0.016376325 254.46413 1 #> result.10 0 1 0 2 0.091279244 97.48479 1 #> result.10 1 1 1 2 0.064984472 160.66696 1 #> 0 0 1 7 0.040942128 227.00361 1 #> result.9 0 0 1 5 0.050569465 185.49095 1 #> 0 1 0 2 0.089521062 29.52722 2 #> 0 1 0 10 -0.007287669 241.64255 2 #> result.7 0 1 0 4 0.046619935 75.54845 2 #> 1 1 1 2 0.086513902 62.69761 2 #> 1 1 1 7 0.029269549 171.27810 2 #> result.8 1 1 1 6 0.045637835 122.55207 2 #> 1 1 1 3 0.039683388 145.01987 2 #> result.14 1 1 1 7 0.021283369 224.89984 2 #> result.12 1 1 1 10 0.022574382 222.37007 2 #> CrowD #> result.7 Inf #> Inf #> result.10 0.9381609 #> result.10 0.6797534 #> 0.5511496 #> result.9 0.4589268 #> Inf #> Inf #> result.7 0.5684247 #> 0.5230166 #> 0.4472203 #> result.8 0.3338430 #> 0.3267032 #> result.14 0.3173944 #> result.12 0.2788557 #> #> 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 14.498664 #> result.14 0.021283369 224.899836 #> result.10 0.091279244 97.484791 #> result.10 0.064984472 160.666960 #> result.9 0.050569465 185.490954 #> result.12 0.022574382 222.370070 #> result.8 0.006243922 195.697243 #> result.1 0.066353108 1.783561 #> result.15 0.009783651 142.755291 #> result.8 0.045637835 122.552069 #> result.7 0.046619935 75.548449 #> result.3 0.058048682 36.272757 #> result.13 0.051706671 48.160610 #> result.6 0.052897230 18.820122 #> result.14 0.030435647 121.988320 #> #> [[3]] #> #> result.7 0.108880468 14.498664 #> 0.016376325 254.464130 #> result.10 0.091279244 97.484791 #> result.10 0.064984472 160.666960 #> result.9 0.050569465 185.490954 #> result.12 0.022574382 222.370070 #> result.14 0.021283369 224.899836 #> result.8 0.006243922 195.697243 #> 0.086300777 46.314727 #> 0.029269549 171.278104 #> result.13 0.051706671 48.160610 #> result.7 0.046619935 75.548449 #> 0.039683388 145.019866 #> result.8 0.045637835 122.552069 #> result.1 0.066353108 1.783561 #> #> [[4]] #> #> result.7 0.108880468 14.49866 #> 0.016376325 254.46413 #> result.10 0.091279244 97.48479 #> result.10 0.064984472 160.66696 #> result.9 0.050569465 185.49095 #> result.12 0.022574382 222.37007 #> result.14 0.021283369 224.89984 #> 0.089521062 29.52722 #> -0.007287669 241.64255 #> result.7 0.046619935 75.54845 #> 0.086513902 62.69761 #> 0.014510663 217.47954 #> result.8 0.045637835 122.55207 #> 0.039683388 145.01987 #> 0.029269549 171.27810 #> #> [[5]] #> #> result.7 0.108880468 14.49866 #> 0.016376325 254.46413 #> result.10 0.091279244 97.48479 #> result.10 0.064984472 160.66696 #> 0.040942128 227.00361 #> result.9 0.050569465 185.49095 #> 0.089521062 29.52722 #> -0.007287669 241.64255 #> result.7 0.046619935 75.54845 #> 0.086513902 62.69761 #> 0.029269549 171.27810 #> result.8 0.045637835 122.55207 #> 0.039683388 145.01987 #> result.14 0.021283369 224.89984 #> result.12 0.022574382 222.37007 #> #>