View source: R/capacity_logreg_testing.R

capacity_logreg_testing | R Documentation |

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
)
```

`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. |

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).

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

[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.

```
## 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)
```

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