capacity_logreg_testing function

Testing procedures for estimation of channel capacity

Diagnostic procedures that allows to compute the uncertainty of estimation of channel capacity by SLEMI approach. Two main procedures are implemented: bootstrap, which execute estimation with using a fraction of data and overfitting test, which divides data into two parts: training and testing. Each of them is repeated specified number of times to obtain a distribution of our estimators. It is recommended to conduct estimation by calling capacity_logreg_main.R.

capacity_logreg_testing(
  data,
  signal = "signal",
  response = "response",
  side_variables = NULL,
  cc_maxit = 100,
  lr_maxit = 1000,
  MaxNWts = 5000,
  formula_string = NULL,
  TestingSeed = 1234,
  testing_cores = 1,
  boot_num = 10,
  boot_prob = 0.8,
  sidevar_num = 10,
  traintest_num = 10,
  partition_trainfrac = 0.6
)

Arguments

• data: must be a data.frame object. Cannot contain NA values.
• signal: is a character object with names of columns of dataRaw to be treated as channel's input.
• response: is a character vector with names of columns of dataRaw to be treated as channel's output
• side_variables: (optional) is a character vector that indicates side variables' columns of data, if NULL no side variables are included
• cc_maxit: is the number of iteration of iterative optimisation of the algorithm to estimate channel capacity. Default is 100.
• lr_maxit: is a maximum number of iteration of fitting algorithm of logistic regression. Default is 1000.
• MaxNWts: is a maximum acceptable number of weights in logistic regression algorithm. Default is 5000.
• formula_string: (optional) is a character object that includes a formula syntax to use in logistic regression model. If NULL, a standard additive model of response variables is assumed. Only for advanced users.
• TestingSeed: is the seed for random number generator used in testing procedures
• testing_cores: - number of cores to be used in parallel computing (via doParallel package)
• boot_num: is the number of bootstrap tests to be performed. Default is 10, but it is recommended to use at least 50 for reliable estimates.
• boot_prob: is the proportion of initial size of data to be used in bootstrap. Default is 0.8.
• sidevar_num: is the number of re-shuffling tests of side variables to be performed. Default is 10, but it is recommended to use at least 50 for reliable estimates.
• traintest_num: is the number of overfitting tests to be performed. Default is 10, but it is recommended to use at least 50 for reliable estimates.
• partition_trainfrac: is the fraction of data to be used as a training dataset. Default is 0.6.

Returns

a list with four elements:

• output$bootstrap - confusion matrix of logistic regression predictions
• output$resamplingMorph - channel capacity in bits
• output$traintest - optimal probability distribution
• output$bootResampMorph - nnet object describing logistic regression model (if model_out=TRUE)

Each of above is a list, where an element is an output of a single repetition of the channel capacity algorithm

Details

If side variables are added within the analysis (side_variables is not NULL), two additional procedures are carried out: reshuffling test and reshuffling with bootstrap test, which are based on permutation of side variables values within the dataset. Additional parameters: lr_maxit and MaxNWts are the same as in definition of multinom function from nnet package. An alternative model formula (using formula_string arguments) should be provided if data are not suitable for description by logistic regression (recommended only for advanced users).

References

[1] Jetka T, Nienaltowski K, Winarski T, Blonski S, Komorowski M, Information-theoretic analysis of multivariate single-cell signaling responses using SLEMI, PLoS Comput Biol, 15(7): e1007132, 2019, https://doi.org/10.1371/journal.pcbi.1007132.

Examples

## Please set boot_num and traintest_num with larger numbers 
## for a more reliable testing
tempdata=data_example1
outputCLR1_testing=capacity_logreg_testing(data=tempdata,
signal="signal", response="response",cc_maxit=10,
TestingSeed=11111, boot_num=1,boot_prob=0.8,testing_cores=1,
traintest_num=1,partition_trainfrac=0.6)