R/callback-functions.R
no_report_callback.RdThe main idea behind this callback function is to provide some feedback to the user about galgo execution. No other relevant information is shown
no_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 no_report_callback assigned to the report_callback # hook-point galgoR::galgo(generations = 5, population = 15, prob_matrix = expression, OS = OS, report_callback = no_report_callback )#>#> ....*#> An object of class "galgo.Obj" #> Slot "Solutions": #> 203506_s_at 209660_at 38043_at 216018_at 206434_at 213141_at #> result.8 0 1 1 1 1 1 #> 0 0 0 0 1 0 #> 1 1 0 0 0 1 #> result.14 1 0 1 1 0 1 #> result.9 1 1 1 1 1 1 #> result.7 0 0 0 0 0 0 #> 1 1 1 1 1 1 #> result.8 0 1 0 0 1 1 #> result.1 0 1 0 1 0 1 #> 1 1 1 1 1 1 #> 0 1 1 1 1 1 #> result.12 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> result.10 1 1 1 1 1 1 #> result.1 0 1 0 0 0 0 #> 201836_s_at 222011_s_at 219114_at 215902_at 210233_at 214820_at #> result.8 1 1 1 1 1 1 #> 0 0 1 0 0 0 #> 0 0 1 0 0 0 #> result.14 1 1 1 0 1 1 #> result.9 0 1 1 1 1 0 #> result.7 0 0 1 0 0 0 #> 1 1 1 1 1 1 #> result.8 0 1 1 0 1 1 #> result.1 1 1 1 1 0 0 #> 1 1 1 1 1 1 #> 1 1 1 1 1 1 #> result.12 1 1 1 0 1 1 #> 1 1 1 1 1 1 #> result.10 1 1 1 1 1 1 #> result.1 1 1 1 0 0 0 #> 200679_x_at 219600_s_at 206317_s_at 219014_at 204957_at 214245_at #> result.8 1 1 1 1 1 1 #> 0 0 1 0 0 1 #> 0 0 0 0 0 0 #> result.14 1 0 1 1 1 1 #> result.9 1 1 0 1 1 1 #> result.7 0 0 1 0 0 1 #> 1 1 0 1 1 1 #> result.8 0 0 1 0 0 1 #> result.1 0 0 0 0 1 1 #> 1 0 1 1 1 1 #> 1 1 1 1 1 1 #> result.12 0 0 0 1 1 0 #> 0 0 0 1 1 0 #> result.10 1 0 0 1 1 1 #> result.1 0 0 0 0 1 0 #> 215755_at 204335_at 200639_s_at 211026_s_at 218461_at 202524_s_at #> result.8 1 1 1 1 1 1 #> 0 1 0 0 0 0 #> 0 0 1 0 0 1 #> result.14 0 1 1 1 1 1 #> result.9 1 1 1 1 0 0 #> result.7 0 1 0 0 0 0 #> 0 1 1 1 0 1 #> result.8 1 1 0 1 0 0 #> result.1 0 0 1 1 0 0 #> 0 1 1 1 0 1 #> 1 1 1 1 1 1 #> result.12 0 1 1 1 0 1 #> 0 1 1 1 0 1 #> result.10 0 1 1 1 0 1 #> result.1 0 0 0 1 0 0 #> 204433_s_at 215799_at 206586_at 202068_s_at 205177_at 203355_s_at #> result.8 1 1 1 1 1 0 #> 0 0 0 0 0 0 #> 0 0 1 1 1 0 #> result.14 1 0 0 1 1 1 #> result.9 0 0 1 1 1 1 #> result.7 0 0 0 0 0 0 #> 1 0 0 0 0 1 #> result.8 1 0 1 0 0 0 #> result.1 0 0 0 0 0 1 #> 1 1 1 0 1 0 #> 1 1 1 1 0 1 #> result.12 1 0 0 0 0 1 #> 1 1 0 0 0 1 #> result.10 1 1 1 0 0 1 #> result.1 0 0 0 0 0 0 #> 210831_s_at 217779_s_at 204654_s_at 220190_s_at 203818_s_at #> result.8 1 1 1 1 1 #> 0 1 0 0 0 #> 0 1 0 0 0 #> result.14 0 1 1 0 1 #> result.9 0 1 1 1 1 #> result.7 0 1 0 0 0 #> 1 1 1 1 1 #> result.8 0 1 1 0 1 #> result.1 0 1 0 1 1 #> 1 1 1 1 1 #> 1 1 1 1 1 #> result.12 0 1 1 0 1 #> 0 1 1 0 1 #> result.10 1 1 1 1 1 #> result.1 0 1 0 1 1 #> 210961_s_at 203234_at 222247_at 210576_at 210781_x_at 213855_s_at #> result.8 1 1 1 1 1 1 #> 1 0 0 0 0 0 #> 0 0 0 0 0 0 #> result.14 1 1 1 0 1 0 #> result.9 1 0 1 1 1 1 #> result.7 0 0 0 0 0 0 #> 0 1 1 1 1 1 #> result.8 0 0 1 0 0 0 #> result.1 0 1 1 1 1 1 #> 1 1 1 0 1 0 #> 1 1 1 1 1 1 #> result.12 0 1 1 0 1 0 #> 1 1 0 0 1 0 #> result.10 1 1 1 0 1 0 #> result.1 0 1 0 0 1 1 #> 218324_s_at 201058_s_at 218667_at 211775_x_at 208406_s_at 204100_at #> result.8 1 1 1 1 1 1 #> 0 0 0 0 0 0 #> 1 0 1 0 1 0 #> result.14 1 0 1 0 1 1 #> result.9 1 0 1 0 1 1 #> result.7 0 0 0 0 0 0 #> 1 0 1 0 1 1 #> result.8 0 1 1 0 0 1 #> result.1 0 0 1 0 0 1 #> 1 1 1 0 1 1 #> 1 1 1 1 1 1 #> result.12 1 0 1 0 1 1 #> 1 1 1 0 1 1 #> result.10 1 0 1 0 1 1 #> result.1 0 0 0 0 0 0 #> 214201_x_at 207916_at 200752_s_at 220024_s_at 213346_at 217931_at #> result.8 1 1 1 1 1 1 #> 0 0 1 0 1 1 #> 0 0 0 0 0 0 #> result.14 1 1 0 1 0 0 #> result.9 1 0 0 1 1 1 #> result.7 0 0 1 0 1 1 #> 1 1 1 1 0 0 #> result.8 1 0 1 1 1 1 #> result.1 0 0 0 1 1 0 #> 1 0 0 1 0 0 #> 1 1 1 1 0 1 #> result.12 1 1 0 1 0 0 #> 1 0 0 1 0 0 #> result.10 1 0 0 1 0 0 #> result.1 0 1 0 0 1 0 #> 206947_at 216035_x_at 217665_at 213421_x_at 209903_s_at 202592_at #> result.8 1 1 1 1 1 1 #> 0 0 0 0 0 0 #> 0 0 0 0 0 0 #> result.14 1 1 1 0 1 0 #> result.9 1 1 1 1 0 0 #> result.7 0 0 0 0 0 0 #> 1 1 1 0 1 1 #> result.8 0 0 1 1 0 1 #> result.1 0 0 1 1 0 1 #> 0 1 1 1 0 1 #> 1 1 1 0 1 1 #> result.12 1 1 1 0 1 0 #> 1 1 1 0 0 1 #> result.10 0 1 1 0 0 1 #> result.1 0 0 0 0 0 0 #> 202008_s_at 217977_at 207389_at 212443_at 202258_s_at 55065_at #> result.8 1 1 1 1 0 0 #> 0 0 0 0 0 0 #> 0 0 0 0 1 0 #> result.14 1 0 1 0 1 0 #> result.9 1 1 1 0 1 1 #> result.7 0 0 0 0 0 0 #> 1 0 1 1 1 1 #> result.8 1 0 1 1 0 0 #> result.1 1 1 1 0 1 1 #> 1 1 1 0 1 0 #> 1 0 1 1 1 0 #> result.12 1 0 1 0 1 1 #> 1 0 1 0 1 1 #> result.10 1 0 1 0 1 0 #> result.1 1 0 0 0 1 1 #> 205702_at 219902_at 218560_s_at 203836_s_at 209561_at 211632_at #> result.8 1 1 1 1 1 1 #> 0 0 0 1 0 1 #> 1 0 0 1 0 0 #> result.14 1 0 0 1 1 1 #> result.9 1 1 1 0 0 1 #> result.7 0 0 0 0 0 1 #> 0 0 0 1 1 1 #> result.8 0 0 0 0 1 1 #> result.1 1 0 1 1 0 0 #> 1 0 0 1 1 1 #> 1 1 0 1 1 1 #> result.12 0 0 0 1 1 1 #> 1 0 0 1 1 1 #> result.10 1 0 0 1 1 1 #> result.1 0 0 1 1 0 0 #> 201911_s_at 210794_s_at 210153_s_at 208266_at 218047_at 206716_at #> result.8 1 1 1 1 1 1 #> 0 1 0 0 0 1 #> 0 0 1 1 0 0 #> result.14 1 1 1 1 1 1 #> result.9 1 1 0 1 1 0 #> result.7 0 1 0 0 0 1 #> 1 1 1 1 1 1 #> result.8 0 1 0 0 0 1 #> result.1 0 1 1 0 0 0 #> 1 1 0 1 1 1 #> 1 1 0 1 1 1 #> result.12 1 1 1 0 1 1 #> 1 1 0 0 1 1 #> result.10 1 1 0 1 1 1 #> result.1 0 0 0 0 0 0 #> 214962_s_at 209959_at 209367_at 212834_at 218831_s_at 211490_at #> result.8 0 1 1 0 1 1 #> 0 1 0 0 0 0 #> 0 0 0 0 0 1 #> result.14 1 1 1 0 1 0 #> result.9 1 1 0 1 0 0 #> result.7 0 1 0 0 0 1 #> 1 1 0 0 0 0 #> result.8 0 1 0 1 1 1 #> result.1 1 0 1 1 0 1 #> 1 1 1 0 1 0 #> 1 1 1 0 0 1 #> result.12 1 1 0 0 0 0 #> 1 1 0 0 0 0 #> result.10 1 1 1 0 1 0 #> result.1 1 0 0 1 0 1 #> 218238_at 221676_s_at 218573_at 213875_x_at 206990_at 222153_at #> result.8 1 1 1 1 1 1 #> 0 1 0 0 0 0 #> 0 0 0 0 0 0 #> result.14 0 1 1 1 0 0 #> result.9 0 0 1 1 0 0 #> result.7 0 0 0 0 0 0 #> 0 1 1 0 0 0 #> result.8 1 1 1 1 0 0 #> result.1 1 0 0 0 1 0 #> 1 1 1 1 1 0 #> 1 1 1 1 1 0 #> result.12 0 1 1 0 0 0 #> 0 1 1 0 1 0 #> result.10 0 1 1 1 1 0 #> result.1 1 0 0 0 0 0 #> 202494_at 201149_s_at 216224_s_at 201222_s_at 213189_at 211605_s_at #> result.8 1 1 1 1 1 1 #> 0 0 0 0 0 0 #> 0 0 1 0 0 1 #> result.14 0 1 0 0 1 1 #> result.9 1 0 0 1 1 0 #> result.7 0 0 0 0 0 0 #> 1 0 1 0 1 1 #> result.8 1 0 1 1 0 0 #> result.1 1 0 0 0 0 1 #> 0 1 0 0 1 1 #> 1 1 1 1 1 1 #> result.12 0 0 0 0 1 1 #> 0 0 0 0 1 1 #> result.10 0 1 0 0 1 1 #> result.1 0 0 0 0 0 1 #> 216788_at 209669_s_at 210632_s_at 214719_at 208947_s_at k #> result.8 1 1 1 1 1 10 #> 0 0 0 0 1 2 #> 0 0 0 0 0 4 #> result.14 1 1 1 0 1 7 #> result.9 1 1 1 1 1 6 #> result.7 0 0 0 0 0 2 #> 1 1 1 0 1 10 #> result.8 0 0 1 0 0 2 #> result.1 0 0 0 0 1 5 #> 0 1 1 0 1 2 #> 1 1 1 1 1 10 #> result.12 0 1 1 0 1 8 #> 0 1 1 0 1 2 #> result.10 0 1 1 0 1 5 #> result.1 0 0 0 0 0 5 #> rnkIndex CrowD #> result.8 -0.003626591 329.1283 1 Inf #> 0.117963145 186.1210 1 Inf #> 0.073046537 222.6191 1 0.8689906 #> result.14 0.029276277 265.3073 1 0.5919964 #> result.9 0.022268603 298.9930 1 0.4272188 #> result.7 0.109268162 102.6672 2 Inf #> 0.010013861 221.8478 2 Inf #> result.8 0.083748461 176.5009 2 0.6581919 #> result.1 0.023328683 191.8677 2 0.6249388 #> 0.097478327 148.1222 2 0.4054109 #> 0.013241080 217.7946 2 0.1855238 #> result.12 0.004524431 208.2488 3 Inf #> 0.096284133 83.4890 3 Inf #> result.10 0.061084953 131.8985 3 0.4137383 #> result.1 0.035675144 162.3784 3 0.4018746 #> #> Slot "ParetoFront": #> [[1]] #> [,1] [,2] #> result.1 0.0356751436 162.378445 #> result.2 -0.0002325493 25.084800 #> result.3 -0.0157067264 126.132170 #> result.4 0.0138296688 39.080717 #> result.5 0.0444034647 137.437453 #> result.6 0.0088833112 99.629015 #> result.7 0.1092681622 102.667236 #> result.8 -0.0036265908 329.128315 #> result.9 0.0222686031 298.993005 #> result.10 0.0079519723 18.104396 #> result.11 0.0445516886 5.563439 #> result.12 0.0252553505 26.437668 #> result.13 0.0429342871 88.308006 #> result.14 0.0613397992 86.145788 #> result.15 0.0311017835 82.984682 #> #> [[2]] #> #> result.7 0.109268162 102.66724 #> result.8 -0.003626591 329.12832 #> result.8 0.083748461 176.50095 #> result.14 0.029276277 265.30734 #> result.9 0.022268603 298.99301 #> result.14 0.061339799 86.14579 #> result.12 0.004524431 208.24875 #> result.1 0.023328683 191.86774 #> result.1 0.035675144 162.37844 #> result.5 0.044403465 137.43745 #> result.10 0.061084953 131.89851 #> result.5 0.049949305 21.44234 #> result.15 -0.017504952 161.87653 #> result.3 0.019716226 116.98455 #> result.13 0.042934287 88.30801 #> #> [[3]] #> #> result.7 0.109268162 102.66724 #> result.8 -0.003626591 329.12832 #> 0.073046537 222.61912 #> result.14 0.029276277 265.30734 #> result.9 0.022268603 298.99301 #> 0.097478327 148.12216 #> result.8 0.083748461 176.50095 #> result.12 0.004524431 208.24875 #> 0.096284133 83.48900 #> result.14 0.061339799 86.14579 #> result.1 0.023328683 191.86774 #> result.1 0.035675144 162.37844 #> result.5 0.044403465 137.43745 #> result.10 0.061084953 131.89851 #> -0.009369553 182.34447 #> #> [[4]] #> #> result.8 -0.003626591 329.12832 #> 0.117963145 186.12102 #> 0.073046537 222.61912 #> result.14 0.029276277 265.30734 #> result.9 0.022268603 298.99301 #> result.7 0.109268162 102.66724 #> 0.013241080 217.79465 #> result.8 0.083748461 176.50095 #> result.1 0.023328683 191.86774 #> 0.097478327 148.12216 #> result.12 0.004524431 208.24875 #> 0.096284133 83.48900 #> result.1 0.035675144 162.37844 #> result.14 0.061339799 86.14579 #> result.10 0.061084953 131.89851 #> #> [[5]] #> #> result.8 -0.003626591 329.1283 #> 0.117963145 186.1210 #> 0.073046537 222.6191 #> result.14 0.029276277 265.3073 #> result.9 0.022268603 298.9930 #> result.7 0.109268162 102.6672 #> 0.010013861 221.8478 #> result.8 0.083748461 176.5009 #> result.1 0.023328683 191.8677 #> 0.097478327 148.1222 #> 0.013241080 217.7946 #> result.12 0.004524431 208.2488 #> 0.096284133 83.4890 #> result.10 0.061084953 131.8985 #> result.1 0.035675144 162.3784 #> #>