# BinaryLogBiplotGD: Binary Logistic Biplot with Gradient Descent Estimation In MultBiplotR: Multivariate Analysis Using Biplots in R

 BinaryLogBiplotGD R Documentation

## Binary Logistic Biplot with Gradient Descent Estimation

### Description

Binary Logistic Biplot with Gradient Descent Estimation. An external optimization function is used to calculate the parameters.

### Usage

``````BinaryLogBiplotGD(X, freq = matrix(1, nrow(X), 1), dim = 2, tolerance =
1e-07, penalization = 0.01, num_max_iters = 100,
RotVarimax = FALSE, seed = 0, OptimMethod = "CG",
Initial = "random", Orthogonalize = FALSE, Algorithm =
"Joint", ...)
``````

### Arguments

 `X` A binary data matrix `freq` Frequencies of each row. When adequate. `dim` Dimension of the final solution. `tolerance` Tolerance for convergence of the algorithm. `penalization` Ridge penalization constant. `num_max_iters` Maximum number of iterations of the algorithm. `RotVarimax` Should the final solution be rotated. `seed` Seed for the random numbers. Used for reproductibility. `OptimMethod` Optimization method used by `optim`. `Initial` Initial configuration to start the iterations. `Orthogonalize` Should te solution be orthogonalized?. `Algorithm` Algorithm for esimation: Joint or alternated. `...` Aditional parameters used by the optimization function.

### Details

Fits a binary logistic biplot using gradient descent. The general function `optim` is used to optimize the loss function. Conjugate gradien is used as a default although other alternatives can be USED.

### Value

An object of class "Binary.Logistic.Biplot".

### Author(s)

Jose Luis Vicente-Villardon

### References

Vicente-Villardon, J. L., Galindo, M. P. and Blazquez, A. (2006) Logistic Biplots. In Multiple Correspondence Análisis And Related Methods. Grenacre, M & Blasius, J, Eds, Chapman and Hall, Boca Raton.

Demey, J., Vicente-Villardon, J. L., Galindo, M.P. AND Zambrano, A. (2008) Identifying Molecular Markers Associated With Classification Of Genotypes Using External Logistic Biplots. Bioinformatics, 24(24): 2832-2838.

### Examples

``````data(spiders)
X=Dataframe2BinaryMatrix(spiders)

logbip=BinaryLogBiplotGD(X,penalization=0.1)
plot(logbip, Mode="a")
summary(logbip)
``````

MultBiplotR documentation built on Nov. 21, 2023, 5:08 p.m.