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SIMPLICA (version 1.0.0)

Biclustering via Simplivariate Component Analysis

Description

Identifies constant, additive, multiplicative, and user-defined simplivariate components in numeric data matrices using a genetic algorithm. Supports flexible pattern definitions and provides visualization for general biclustering applications across diverse domains. The method builds on simplivariate models as introduced in Hageman et al. (2008) and is related to biclustering frameworks as reviewed by Madeira and Oliveira (2004) .

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install.packages('SIMPLICA')

Monthly Downloads

112

Version

1.0.0

License

GPL-3

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Maintainer

Jos Hageman

Last Published

September 3rd, 2025

Functions in SIMPLICA (1.0.0)

plotComponentResult

Plot non-contiguous simplivariate components by pattern type, with optional reordering
print.summaryComponents

Print method for summaryComponents
simplica

SIMPLICA: Simultaneous Identification of Simplivariate Components
multiplicativeMatrix

Generate an multiplicative approximation of a data matrix
simplicaCV

Test Simplivariate Components with Cross-Validation Pattern Selection
globals

Global Variables Declaration
multiplicativeMatrixFitter

Multiplicative Pattern Fitter
fitnessForOneComponent

Compute best pattern-based fitness for a single Simplivariate Component
fitness

Fitness function with automatic pattern selection per Simplivariate Component
componentCVPatterns

Cross-Validation of Simplivariate Component Patterns
SCAMonitorFactory

Simplivariate Component Analysis monitoring function factory for GA progress
additiveMatrix

Generate an additive approximation of a data matrix
gaintegerOnePointCrossover

One-point crossover operator for integer-encoded genetic algorithms
defaultPatternFitters

Default Pattern Fitters for SIMPLICA
additiveMatrixFitter

Additive Pattern Fitter
gaintegerMutation

Integer mutation operator for genetic algorithms
defaultPatternFunctions

Default pattern generators for SIMPLICA
simplicaToy

Toy matrix with one multiplicative and one additive bicluster
gaintegerPopulationFactory

GA Integer Population Factory
summaryComponents

Summarize GA-found Simplivariate Components