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Table of Contents

SymbolicR

Find non-linear formulas that fits your input data. You can systematically explore and memoize the possible formulas and its cross-validation performance, in an incremental fashon. Three main interoperable search functions are available:

  • random.search performs a random exploration,
  • genetic.search employs a genetic optimization algorithm
  • comb.search allows the user to provide a data.frame of formulas to be tested

After installation, see tutorials by typing

browseVignettes('symbolicr')

in your R console.

Publications

SymbolicR was featured in the following scientific publication as a data-driven approach to refine and extend a mechanistic model of Fc-fusion protein pharmacokinetics:

Tomasoni et al. Predicting Aberrant Fc-fusion Protein Pharmacokinetics from in Silico Structural Properties and Physiologically Based Pharmacokinetic (PBPK) Modeling, The AAPS Journal, March 2026 link

DOI

Installation

You can install the development version of symbolicr like so:

devtools::install_github('cosbi-research/symbolicr', build_vignettes = TRUE)

Genetic search

This is a minimum viable example on how to use genetic search to find the non-linear relationship:

library(symbolicr)
set.seed(1)
# set-up a toy example dataset
x1<-runif(100, min=2, max=67)
x2<-runif(100, min=0.01, max=0.1)
X <- data.frame(x1=x1, x2=x2)
# set up a "true" non-linear relationship
# with some noise
y <- log10(x1^2*x2) + rnorm(100, 0, 0.001)

results <- genetic.search(
  X, y, 
  n.squares=2, 
  max.formula.len = 1, 
  N=2,
  K=10,
  best.vars.l = list(
   c('log.x1')
  ),
  transformations = list(
   "log"=function(rdf, x, stats){ log(x) },
   "inv"=function(rdf, x, stats){ 1/x }
  ),
  keepBest=T,
  cv.norm=F
)
#> ## Total number of single terms: 27
#> Iteration: 1 Mean/Max fitness:-9.80e+07 / 1.66e+00 Best: log.x1
#> Iteration: 2 Mean/Max fitness:-9.80e+07 / 1.66e+00 Best: log.x1
#> Iteration: 3 Mean/Max fitness:-9.80e+07 / 1.66e+00 Best: log.x1
#> Iteration: 4 Mean/Max fitness:-9.60e+07 / 1.66e+00 Best: log.x1
#> Iteration: 5 Mean/Max fitness:-9.40e+07 / 1.66e+00 Best: log.x1
#> Iteration: 6 Mean/Max fitness:-9.40e+07 / 1.66e+00 Best: log.x1
#> Iteration: 7 Mean/Max fitness:-9.40e+07 / 1.66e+00 Best: log.x1
#> Iteration: 8 Mean/Max fitness:-9.40e+07 / 1.66e+00 Best: log.x1
#> Iteration: 9 Mean/Max fitness:-9.60e+07 / 1.66e+00 Best: log.x1
#> Iteration: 10 Mean/Max fitness:-9.60e+07 / 1.66e+00 Best: log.x1
#> Iteration: 11 Mean/Max fitness:-9.60e+07 / 1.66e+00 Best: log.x1
#> Iteration: 12 Mean/Max fitness:-9.60e+07 / 1.66e+00 Best: log.x1
#> Iteration: 13 Mean/Max fitness:-9.40e+07 / 1.66e+00 Best: log.x1
#> Iteration: 14 Mean/Max fitness:-9.40e+07 / 1.66e+00 Best: log.x1
#> Iteration: 15 Mean/Max fitness:-9.60e+07 / 1.66e+00 Best: log.x1
#> Iteration: 16 Mean/Max fitness:-9.40e+07 / 1.66e+00 Best: log.x1
#> Iteration: 17 Mean/Max fitness:-9.60e+07 / 1.66e+00 Best: log.x1
#> Iteration: 18 Mean/Max fitness:-9.40e+07 / 1.66e+00 Best: log.x1
#> Iteration: 19 Mean/Max fitness:-9.00e+07 / 1.69e+00 Best: log.x1
#> Iteration: 20 Mean/Max fitness:-9.60e+07 / 1.69e+00 Best: log.x1
#> Iteration: 21 Mean/Max fitness:-9.00e+07 / 1.69e+00 Best: log.x1
#> Iteration: 22 Mean/Max fitness:-9.40e+07 / 1.69e+00 Best: log.x1
#> Iteration: 23 Mean/Max fitness:-9.40e+07 / 1.69e+00 Best: log.mul.x1.x1
#> Iteration: 24 Mean/Max fitness:-9.60e+07 / 1.69e+00 Best: log.mul.x1.x1
#> Iteration: 25 Mean/Max fitness:-9.60e+07 / 1.69e+00 Best: log.mul.x1.x1
#> Iteration: 26 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 27 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 28 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 29 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 30 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 31 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 32 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 33 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 34 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 35 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 36 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 37 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 38 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 39 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 40 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 41 Mean/Max fitness:-9.20e+07 / 1.71e+00 Best: log.x1
#> Iteration: 42 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 43 Mean/Max fitness:-9.20e+07 / 1.71e+00 Best: log.x1
#> Iteration: 44 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 45 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 46 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 47 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 48 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 49 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 50 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 51 Mean/Max fitness:-9.20e+07 / 1.71e+00 Best: log.x1
#> Iteration: 52 Mean/Max fitness:-9.20e+07 / 1.71e+00 Best: log.x1
#> Iteration: 53 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 54 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 55 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 56 Mean/Max fitness:-9.20e+07 / 1.71e+00 Best: log.x1
#> Iteration: 57 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 58 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 59 Mean/Max fitness:-9.20e+07 / 1.71e+00 Best: log.x1
#> Iteration: 60 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 61 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 62 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 63 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 64 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 65 Mean/Max fitness:-9.40e+07 / 1.71e+00 Best: log.x1
#> Iteration: 66 Mean/Max fitness:-9.60e+07 / 1.71e+00 Best: log.x1
#> Iteration: 67 Mean/Max fitness:-9.40e+07 / 6.22e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 68 Mean/Max fitness:-9.40e+07 / 6.22e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 69 Mean/Max fitness:-9.40e+07 / 6.22e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 70 Mean/Max fitness:-9.20e+07 / 6.22e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 71 Mean/Max fitness:-9.20e+07 / 6.22e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 72 Mean/Max fitness:-9.20e+07 / 6.22e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 73 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 74 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 75 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 76 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 77 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 78 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 79 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 80 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 81 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 82 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 83 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 84 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 85 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 86 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 87 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 88 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 89 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 90 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 91 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 92 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 93 Mean/Max fitness:-9.60e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 94 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 95 Mean/Max fitness:-9.20e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 96 Mean/Max fitness:-9.20e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 97 Mean/Max fitness:-9.20e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 98 Mean/Max fitness:-9.40e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 99 Mean/Max fitness:-9.00e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2
#> Iteration: 100 Mean/Max fitness:-9.20e+07 / 6.23e+00 Best: log.mul.x1.mul.x1.x2

We found the correct non-linear formula starting from an initial guess! We can now get the best formula

results$best
#> [1] "log.mul.x1.mul.x1.x2"

And all the formula the genetic algorithm found to be best at each one of the 100 evolution iterations (last 5 shown for brevity)

results$best.iter[seq(length(results$best.iter)-5,length(results$best.iter))]
#> [[1]]
#> [1] "log.mul.x1.mul.x1.x2"
#> 
#> [[2]]
#> [1] "log.mul.x1.mul.x1.x2"
#> 
#> [[3]]
#> [1] "log.mul.x1.mul.x1.x2"
#> 
#> [[4]]
#> [1] "log.mul.x1.mul.x1.x2"
#> 
#> [[5]]
#> [1] "log.mul.x1.mul.x1.x2"
#> 
#> [[6]]
#> [1] "log.mul.x1.mul.x1.x2"

Note that cv.norm=FALSE means data is used as-is. Before running this example we checked for the non-negativeness of x1^2*x2. If you would like to normalize data to avoid scaling issues just use cv.norm=TRUE but in this case, to avoid computing the log of a negative value, we use this updated transformation function

# NB: function applied to standardized X values!
   #     they can be negative
log.std <- function(x, stats){ log(0.1 + abs(stats$min) + x) }

The stats object contains - min: the minimum of the column values - absmin: the minimum of the absolute values of the columns - absmax: the maximum of the absolute values of the columns - projzero: -mean/sd of the columns, that is the position of the zero in the original, non-normalized space.

Type ?dataset.min.maxs in your R console for further informations.

Random search

This is a minimum viable example on how to use random search to test multiple non-linear relationships, and get a summary of the performances in a data.frame:

random.results <- random.search(
  X, y, 
  n.squares=2, 
  formula.len = 1, 
  N=2,
  K=10,
  transformations = list(
   "log"=function(rdf, x, stats){ log(x) },
   "inv"=function(rdf, x, stats){ 1/x }
  ),
  cv.norm=F
)
#> Regression on mul.x2.mul.x2.x2
#> Regression on log.mul.x1.x2
#> Regression on inv.mul.x1.mul.x2.x2
#> Regression on mul.x1.x1
#> Regression on mul.x1.x2
#> Regression on x2
#> Regression on x1
#> Regression on log.x2
#> Regression on mul.x1.mul.x1.x1
#> Regression on log.mul.x2.x2
#> Regression on inv.mul.x2.x2
#> Regression on inv.x2
#> Regression on inv.mul.x1.mul.x1.x2
#> Regression on log.mul.x1.mul.x2.x2
#> Regression on inv.mul.x2.mul.x2.x2
#> Regression on inv.mul.x1.mul.x1.x1
#> Regression on inv.x1
#> Regression on log.mul.x1.mul.x1.x1
#> Regression on mul.x2.x2
#> Regression on log.mul.x1.mul.x1.x2
#> Regression on inv.mul.x1.x2
#> Regression on log.mul.x2.mul.x2.x2
#> Regression on log.mul.x1.x1
#> Regression on inv.mul.x1.x1
#> Regression on mul.x1.mul.x1.x2
#> Regression on log.x1
#> Regression on mul.x1.mul.x2.x2

You can then inspect results in the resulting data.frame:

random.results[order(random.results$base.r.squared, decreasing = T), ][seq(5), ]
#>         base.pe  base.cor base.r.squared base.max.pe  base.iqr.pe
#> 20 0.0004285218 0.9999988      0.9999976 0.004748987 0.0005285826
#> 2  0.0725826920 0.9536868      0.9095013 1.433554884 0.1219353333
#> 26 0.1038707364 0.9276918      0.8606065 1.093821498 0.0978448963
#> 23 0.1005819365 0.9272320      0.8597596 1.111784453 0.0969222114
#> 18 0.1039579306 0.9261947      0.8578210 1.085202757 0.0888076193
#>    base.max.cooksd base.max.cooksd.name                 vars n.squares
#> 20       0.4515147                   47 log.mul.x1.mul.x1.x2         2
#> 2        0.2559093                   27        log.mul.x1.x2         2
#> 26       0.1554620                   47               log.x1         2
#> 23       0.1542245                   47        log.mul.x1.x1         2
#> 18       0.1567286                   47 log.mul.x1.mul.x1.x1         2
#>    formula.len
#> 20           1
#> 2            1
#> 26           1
#> 23           1
#> 18           1

Combinatorial Search

Search over all non-duplicated combinations of terms taken from an user-supplied list of formulas.

# test the three formula x1, x2 and log(x2)
comb.search(
  X, y, 
  combinations=data.frame(t1=c('x1','x2','log.x2')), 
  N=2,
  K=10,
  transformations = list(
   "log"=function(rdf, x, stats){ log(x) },
   "exp"=function(rdf, x, stats){ exp(x) }
  ),
  cv.norm=F
)
#> Regression on x1
#> Regression on x2
#> Regression on log.x2
#>     base.pe  base.cor base.r.squared base.max.pe base.iqr.pe base.max.cooksd
#> 1 0.1302693 0.8630977     0.74487976    3.080926   0.1708999       0.3215164
#> 2 0.2173972 0.3203810     0.09942148    7.524692   0.1991448       0.1019341
#> 3 0.2215673 0.2952262     0.08528910    7.786758   0.1758801       0.1168211
#>   base.max.cooksd.name   vars n.squares formula.len
#> 1                   47     x1         0           1
#> 2                   47     x2         0           1
#> 3                   47 log.x2         0           1

Analyze formula variables

This code highlights the most-important variables among a list of formulas applied to a given dataset.

max.formula.len=1
transformations=list(
   "log"=function(rdf, x, stats){ log(x) },
   "log_x1_p"=function(rdf, x, stats){ log(rdf$x1 + x) },
   "inv"=function(rdf, x, stats){ 1/x }
)
random.results <- random.search(
  X, y, 
  n.squares=2, 
  formula.len = max.formula.len, 
  N=2,
  K=10,
  transformations = transformations,
  cv.norm=F
)
#> Regression on mul.x1.x1
#> Regression on log.mul.x1.x1
#> Regression on mul.x2.mul.x2.x2
#> Regression on mul.x2.x2
#> Regression on inv.mul.x1.mul.x2.x2
#> Regression on log_x1_p.x1
#> Regression on inv.mul.x2.mul.x2.x2
#> Regression on inv.mul.x1.x1
#> Regression on mul.x1.mul.x1.x1
#> Regression on log_x1_p.mul.x1.mul.x2.x2
#> Regression on inv.mul.x2.x2
#> Regression on inv.x1
#> Regression on inv.x2
#> Regression on mul.x1.mul.x2.x2
#> Regression on x1
#> Regression on mul.x1.mul.x1.x2
#> Regression on x2
#> Regression on mul.x1.x2
#> Regression on log_x1_p.mul.x1.x2
#> Regression on log.mul.x1.mul.x1.x2
#> Regression on log_x1_p.mul.x1.x1
#> Regression on inv.mul.x1.mul.x1.x2
#> Regression on log.x1
#> Regression on inv.mul.x1.x2
#> Regression on log.x2
#> Regression on log_x1_p.mul.x2.mul.x2.x2
#> Regression on inv.mul.x1.mul.x1.x1
#> Regression on log_x1_p.mul.x1.mul.x1.x2
#> Regression on log_x1_p.x2
#> Regression on log_x1_p.mul.x2.x2
#> Regression on log.mul.x1.x2
#> Regression on log.mul.x2.x2
#> Regression on log.mul.x1.mul.x2.x2
#> Regression on log.mul.x1.mul.x1.x1
#> Regression on log_x1_p.mul.x1.mul.x1.x1
#> Regression on log.mul.x2.mul.x2.x2

# compute a unique objective function
random.results$obj <- apply(random.results, MARGIN=1, FUN=function(row) pe.r.squared.formula.len.fitness(as.data.frame(t(row)), max.formula.len))

# sort by top-N functions (according to obj)
ordered.res <- random.results[order(random.results$obj,decreasing=T),]

# max fitness on all computed formulas
best.obj <- ordered.res[1,'obj']
# analyze top-10 formulas
# select formulas according to criterion above
eligible.res <- ordered.res[seq(10), ]

direction = 'max' # obj should be maximized
sensitivity <- analyze.variables(
 X, y, eligible.res, fitness.column='obj',
 # a list of available term transformations
 transformations=transformations,
 # a list of rules to remove a variable from a term
 # ex.
 #   orig transformation -> base transformation, removed term
 #   "log_empty_well_p"=c("log10", "empty_well")
 transformations_replacement_map=list(
   "log_x1_p"=c("log", "x1")
 ),
 custom.abs.mins=list(),
 K=10,
 N=2,
 direction=direction, 
 max.formula.len=max.formula.len,
 fitness.fun=pe.r.squared.formula.len.fitness,
 cv.norm=F
)
#> Analyzing log.mul.x1.mul.x1.x2
#> Regression on log.mul.x1.x2
#> Regression on log.mul.x1.x2
#> Regression on log.mul.x1.x1
#> Analyzing log_x1_p.mul.x1.mul.x1.x2
#> Regression on log.mul.x1.mul.x1.x2
#> Regression on log_x1_p.mul.x1.x2
#> Regression on log_x1_p.mul.x1.x2
#> Regression on log_x1_p.mul.x1.x1
#> Analyzing log.mul.x1.x2
#> Regression on log.x2
#> Regression on log.x1
#> Analyzing log_x1_p.mul.x1.x2
#> Regression on log.mul.x1.x2
#> Regression on log_x1_p.x2
#> Regression on log_x1_p.x1
#> Analyzing log_x1_p.x2
#> Regression on log.x2
#> Analyzing log_x1_p.mul.x1.mul.x2.x2
#> Regression on log.mul.x1.mul.x2.x2
#> Regression on log_x1_p.mul.x2.x2
#> Regression on log_x1_p.mul.x1.x2
#> Regression on log_x1_p.mul.x1.x2
#> Warning in rbind(deparse.level, ...): number of columns of result, 3, is not a
#> multiple of vector length 2 of arg 1
#> Analyzing log_x1_p.x1
#> Regression on log.x1
#> Analyzing log.mul.x1.mul.x1.x1
#> Regression on log.mul.x1.x1
#> Regression on log.mul.x1.x1
#> Regression on log.mul.x1.x1
#> Analyzing log_x1_p.mul.x1.mul.x1.x1
#> Regression on log.mul.x1.mul.x1.x1
#> Regression on log_x1_p.mul.x1.x1
#> Regression on log_x1_p.mul.x1.x1
#> Regression on log_x1_p.mul.x1.x1
#> Warning in rbind(deparse.level, ...): number of columns of result, 3, is not a
#> multiple of vector length 4 of arg 1
#> Analyzing log_x1_p.mul.x2.mul.x2.x2
#> Regression on log.mul.x2.mul.x2.x2
#> Regression on log_x1_p.mul.x2.x2
#> Regression on log_x1_p.mul.x2.x2
#> Regression on log_x1_p.mul.x2.x2

# plottable data.frame of quantile losses per-variable
variable.importance.df <- sensitivity[['var.imp']]
n.formulas <- 10
#### PLOT ANALYSIS ####
library(ggplot2)
#> Warning: package 'ggplot2' was built under R version 4.5.2
library(RColorBrewer)
library(colorspace)
#> Warning: package 'colorspace' was built under R version 4.5.2

colours <- brewer.pal(11, "Paired")
cols_d4 <- darken(colours, 0.4)

#png(file.path('sensitivity', paste("sensitivity.",(percent.limit*100),"percent",type,".png", sep = "")), width = 640, height = 490)
p <- ggplot(variable.importance.df, aes(x=mean.occurrences, y=mean.loss.p, colour=variable)) +
  theme(
    text = element_text(size = 15)
  ) +
  labs(x = paste0("Mean number of occurrences for best ",n.formulas," formulas"), y = "relative loss %") +
  #  geom_crossbar(aes(ymin = lower.loss.p, ymax = higher.loss.p), width = 1.5) +
  geom_pointrange(aes(ymin = lower.loss.p, ymax = higher.loss.p)) +
  scale_y_continuous(trans = 'log10', limits=c(1,110), n.breaks=8,
                     labels =c("1%","3%","5%", "10%", "20%", "30%", "50%", "100%"),
                     breaks =c(1, 3, 5, 10, 20, 30, 50, 100))+
  scale_x_continuous(limits=c(0,3.05), n.breaks=6,
                     labels =c("1/5", "1/2", "3/4", "1", "2", "3"),
                     breaks =c(1/5.0, 1/2.0, 3/4.0, 1, 2, 3))+
  scale_color_manual(values = cols_d4)

print(p)

This plot is showing clearly that variable x1 is much more important than variable x2 as it both

  • occours more often in the top-10 formulas, (value on the X axis)
  • degrades the performance more when removed from formulas (value on the Y axis)

About

❗ This is a read-only mirror of the CRAN R package repository. symbolicr — Symbolic Regression Framework. Homepage: https://github.com/cosbi-research/symbolicr Report bugs for this package: https://github.com/cosbi-research/symbolicr/issues

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