Package 'LDABiplots'

Title: Biplot Graphical Interface for LDA Models
Description: Contains the development of a tool that provides a web-based graphical user interface (GUI) to perform Biplots representations from a scraping of news from digital newspapers under the Bayesian approach of Latent Dirichlet Assignment (LDA) and machine learning algorithms. Contains LDA methods described by Blei , David M., Andrew Y. Ng and Michael I. Jordan (2003) <https://jmlr.org/papers/volume3/blei03a/blei03a.pdf>, and Biplot methods described by Gabriel K.R(1971) <doi:10.1093/biomet/58.3.453> and Galindo-Villardon P(1986) <https://diarium.usal.es/pgalindo/files/2012/07/Questiio.pdf>.
Authors: Luis Pilacuan-Bonete [cre, aut] , Purificacion Galindo-Villardón [aut] , Javier De La Hoz Maestre [aut] , Francisco Javier Delgado-Álvarez [aut]
Maintainer: Luis Pilacuan-Bonete <[email protected]>
License: GPL-3
Version: 0.1.2
Built: 2025-02-28 05:19:45 UTC
Source: https://github.com/cran/LDABiplots

Help Index

Pearson Correlation for Sparse Matrices

Description

Pearson Correlation for Sparse Matrices. More memory and time-efficient than cor(as.matrix(x)).

Usage

dtmcorr(x)

Arguments

x

A matrix, potentially a sparse matrix such as a "dgCMatrix" object

Value

a correlation matrix

Remove terms from a Document-Term-Matrix and documents with no terms based on the term frequency inverse document frequency

Description

Remove terms from a Document-Term-Matrix and documents with no terms based on the term frequency inverse document frequency. Either giving in the maximum number of terms (argument top), the tfidf cutoff (argument cutoff) or a quantile (argument prob)

Usage

dtmremovetfidf(dtm, top, cutoff, prob, remove_emptydocs = TRUE)

Arguments

dtm

an object class "dgCMatrix"
top

integer with the number of terms which should be kept as defined by the highest mean tfidf
cutoff

numeric cutoff value to keep only terms in dtm where the tfidf obtained by dtmtfidf is higher than this value
prob

numeric quantile indicating to keep only terms in dtm where the tfidf obtained by dtmtfidf is higher than the prob percent quantile
remove_emptydocs

logical indicating to remove documents containing no more terms after the term removal is executed. Defaults to TRUE.

Value

a sparse Matrix as returned by sparseMatrix where terms with high tfidf are kept and documents without any remaining terms are removed

Term Frequency - Inverse Document Frequency calculation

Description

Term Frequency - Inverse Document Frequency calculation. Averaged by each term.

Usage

dtmtfidf(dtm)

Arguments

dtm

an object class "dgCMatrix"

Value

a vector with tfidf values, one for each term in the dtm matrix

GHBiplot

Description

This function performs the representation of GHBiplot (Gabriel,1971).

Usage

GHBiplot (X, Transform.Data = 'scale')

Arguments

X

array_like;
A data frame which provides the data to be analyzed. All the variables must be numeric.
Transform.Data

character;
A value indicating whether the columns of X (variables) should be centered or scaled. The options are: "center" if center is TRUE, centering is done by subtracting the column means (omitting NA) of x from their corresponding columns, and if center is FALSE, centering is not done. "scale" the value of scale determines how column scaling is performed (after centering). If scale is a numeric-alike vector with length equal to the number of columns of x, then each column of x is divided by the corresponding value from scale. If scale is TRUE then scaling is done by dividing the (centered) columns of x by their standard deviations if center is TRUE, and the root mean square otherwise. If scale is FALSE, no scaling is done. To scale by standard deviations without centering, use scale(x,center=FALSE,scale=apply(x,2,sd,na.rm=TRUE)),"center_scale" center=TRUE and scale=TRUE,"none" neither center nor scale is done. The default value is "scale".

Details

Algorithm used to construct the GH Biplot. The Biplot is obtained as result of the configuration of markers for individuals and markers for variables in a reference system defined by the factorial axes resulting from the Decomposition in Singular Values (DVS).

Value

GHBiplot returns a list containing the following components:

eigenvalues

array_like;
vector with the eigenvalues.

explvar

array_like;
an vector containing the proportion of variance explained by the first 1, 2,.,k principal components obtained.

loadings

array_like;
the loadings of the principal components.

coord_ind

array_like;
matrix with the coordinates of individuals.

coord_var

array_like;
matrix with the coordinates of variables.

References

  • Gabriel, K. R. (1971). The Biplot graphic display of matrices with applications to principal components analysis. Biometrika, 58(3), 453-467.

Examples

GHBiplot(mtcars)

HJBiplot

Description

This function performs the representation of HJ Biplot (Galindo, 1986).

Usage

HJBiplot (X, Transform.Data = 'scale')

Arguments

X

array_like;
A data frame which provides the data to be analyzed. All the variables must be numeric.
Transform.Data

character;
A value indicating whether the columns of X (variables) should be centered or scaled. The options are: "center" if center is TRUE, centering is done by subtracting the column means (omitting NA) of x from their corresponding columns, and if center is FALSE, centering is not done. "scale" the value of scale determines how column scaling is performed (after centering). If scale is a numeric-alike vector with length equal to the number of columns of x, then each column of x is divided by the corresponding value from scale. If scale is TRUE then scaling is done by dividing the (centered) columns of x by their standard deviations if center is TRUE, and the root mean square otherwise. If scale is FALSE, no scaling is done. To scale by standard deviations without centering, use scale(x,center=FALSE,scale=apply(x,2,sd,na.rm=TRUE)),"center_scale" center=TRUE and scale=TRUE,"none" neither center nor scale is done. The default value is "scale".

Details

Algorithm used to construct the HJ Biplot. The Biplot is obtained as result of the configuration of markers for individuals and markers for variables in a reference system defined by the factorial axes resulting from the Decomposition in Singular Values (DVS).

Value

HJBiplot returns a list containing the following components:

eigenvalues

array_like;
vector with the eigenvalues.

explvar

array_like;
an vector containing the proportion of variance explained by the first 1, 2,.,k principal components obtained.

loadings

array_like;
the loadings of the principal components.

coord_ind

array_like;
matrix with the coordinates of individuals.

coord_var

array_like;
matrix with the coordinates of variables.

References

  • Gabriel, K. R. (1971). The Biplot graphic display of matrices with applications to principal components analysis. Biometrika, 58(3), 453-467.

  • Galindo-Villardon, P. (1986). Una alternativa de representacion simultanea: HJ-Biplot (An alternative of simultaneous representation: HJ-Biplot). Questiio, 10, 13-23.

Examples

HJBiplot(mtcars)

JKBiplot

Description

This function performs the representation of JK Biplot (Gabriel,1971).

Usage

JKBiplot (X, Transform.Data = 'scale')

Arguments

X

array_like;
A data frame which provides the data to be analyzed. All the variables must be numeric.
Transform.Data

character;
A value indicating whether the columns of X (variables) should be centered or scaled. The options are: "center" if center is TRUE, centering is done by subtracting the column means (omitting NA) of x from their corresponding columns, and if center is FALSE, centering is not done. "scale" the value of scale determines how column scaling is performed (after centering). If scale is a numeric-alike vector with length equal to the number of columns of x, then each column of x is divided by the corresponding value from scale. If scale is TRUE then scaling is done by dividing the (centered) columns of x by their standard deviations if center is TRUE, and the root mean square otherwise. If scale is FALSE, no scaling is done. To scale by standard deviations without centering, use scale(x,center=FALSE,scale=apply(x,2,sd,na.rm=TRUE)),"center_scale" center=TRUE and scale=TRUE,"none" neither center nor scale is done. The default value is "scale".

Details

Algorithm used to construct the JK Biplot. The Biplot is obtained as result of the configuration of markers for individuals and markers for variables in a reference system defined by the factorial axes resulting from the Decomposition in Singular Values (DVS).

Value

JKBiplot returns a list containing the following components:

eigenvalues

array_like;
vector with the eigenvalues.

explvar

array_like;
an vector containing the proportion of variance explained by the first 1, 2,.,k principal components obtained.

loadings

array_like;
the loadings of the principal components.

coord_ind

array_like;
matrix with the coordinates of individuals.

coord_var

array_like;
matrix with the coordinates of variables.

References

  • Gabriel, K. R. (1971). The Biplot graphic display of matrices with applications to principal components analysis. Biometrika, 58(3), 453-467.

Examples

JKBiplot(mtcars)

Plotting Biplot

Description

Plot_Biplot initializes a ggplot2-based visualization of the caracteristics presented in the data analized by the Biplot selected.

Usage

Plot_Biplot(X, axis = c(1,2), hide = "none",
 labels = "auto", ind.shape = 19,
 ind.color = "red", ind.size = 2,
 ind.label = FALSE, ind.label.size = 4,
 var.color = "black", var.size = 0.5,
 var.label = TRUE, var.label.size = 4, var.label.angle = FALSE)

Arguments

X

List containing the output of one of the functions of the package.
axis

Vector with lenght 2 which contains the axis ploted in x and y axis.
hide

Vector specifying the elements to be hidden on the plot. Default value is “none”. Other allowed values are “ind” and “var”.
labels

It indicates the label for points. If it is "auto" the labels are the row names of the coordinates of individuals. If it isn't auto it would be a vector containing the labels.
ind.shape

Points shape. It can be a number to indicate the shape of all the points or a factor to indicate different shapes.
ind.color

Points colors. It can be a character indicating the color of all the points or a factor to use different colors.
ind.size

Size of points.
ind.label

Logical value, if it is TRUE it prints the name for each row of X. If it is FALSE (default) does not print the names.
ind.label.size

Numeric value indicating the size of the labels of points.
var.color

Character indicating the color of the arrows.
var.size

Size of arrow.
var.label

Logical value, if it is TRUE (default) it prints the name for each column of X. If it is FALSE does not print the names.
var.label.size

Numeric value indicating the size of the labels of variables.
var.label.angle

Logical value, if it it TRUE (default) it print the vector names with orentation of the angle of the vector. If it is FALSE the angle of all tags is 0.

Value

Return a ggplot2 object.

See Also

HJBiplot

Examples

hj.biplot <- HJBiplot(mtcars)
Plot_Biplot(hj.biplot, ind.label = TRUE)

Shiny UI for LDABiplots package

Description

Shiny UI for LDABiplots package

Usage

runLDABiplots(host = "127.0.0.1", port = NULL, launch.browser = TRUE)

Arguments

host

The IPv4 address that the application should listen on. Defaults to the shiny.host option, if set, or "127.0.0.1" if not.
port

is the TCP port that the application should listen on. If the port is not specified, and the shiny.port option is set (with options(shiny.port = XX)), then that port will be used. Otherwise, use a random port.
launch.browser

If true, the system's default web browser will be launched automatically after the app is started. Defaults to true in interactive sessions only. This value of this parameter can also be a function to call with the application's URL.

Value

No return value

Examples

if(interactive()){
runLDABiplots()
}