capacity_logreg_testing: Testing procedures for estimation of channel capacity
In SLEMI: Statistical Learning Based Estimation of Mutual Information

View source: R/capacity_logreg_testing.R

capacity_logreg_testing

R Documentation

Testing procedures for estimation of channel capacity

Description

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.

Usage

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.

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).

Value

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

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)

SLEMI documentation built on Nov. 20, 2023, 1:06 a.m.