A default call_back function that does nothing.

default_callback(
  userdir = "",
  generation,
  pop_pool,
  pareto,
  prob_matrix,
  current_time
)

Arguments

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 `data.frame` with the solution vectors, number of clusters and their ranking.
pareto	the solutions found by Galgo across all generations in the solution space
prob_matrix	a `matrix` or `data.frame`. Must be an expression matrix with features in rows and samples in columns
current_time	an `POSIXct` object

Examples

# load example dataset

library(breastCancerTRANSBIG)
data(transbig)
Train <- transbig
rm(transbig)
#> Warning: object 'transbig' not found
expression <- 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 default_callback assigned to all the hook-points

galgoR::galgo(generations = 5,
population = 15,
prob_matrix = expression,
OS = OS,
start_galgo_callback = default_callback, # When Galgo is about to start.
end_galgo_callback = default_callback,   # When Galgo is about to finish. 
start_gen_callback = default_callback,   # At the beginning of each generation/iteration.
end_gen_callback = default_callback,     # At the end of each generation/iteration.
)
#> Using CPU for computing pearson distance
#> Generation 1 Non-dominated solutions:
#>           k                     rnkIndex    CrowD
#> result.1  2 0.13820096 139.3294        1      Inf
#> result.5  9 0.02957247 306.9323        1      Inf
#> result.13 2 0.06096262 155.4601        1 1.423909
#> Generation 2 Non-dominated solutions:
#>          k                     rnkIndex    CrowD
#> result.1 2 0.13820096 139.3294        1      Inf
#> result.5 9 0.02957247 306.9323        1      Inf
#> result.9 2 0.12893556 217.2990        1 1.334205
#> Generation 3 Non-dominated solutions:
#>          k                     rnkIndex    CrowD
#> result.5 9 0.02957247 306.9323        1      Inf
#>          2 0.15361747 200.8407        1      Inf
#> result.9 2 0.12893556 217.2990        1 1.246685
#> Generation 4 Non-dominated solutions:
#>          k                     rnkIndex    CrowD
#> result.5 9 0.02957247 306.9323        1      Inf
#>          2 0.15361747 200.8407        1      Inf
#> result.9 2 0.12893556 217.2990        1 1.181198
#> Generation 5 Non-dominated solutions:
#>          k                     rnkIndex CrowD
#> result.5 9 0.02957247 306.9323        1   Inf
#>          2 0.17671211 231.1517        1   Inf
#> NULL