Package: SIMPLICA 1.0.0

SIMPLICA: Biclustering via Simplivariate Component Analysis

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) <doi:10.1371/journal.pone.0003259> and is related to biclustering frameworks as reviewed by Madeira and Oliveira (2004) <doi:10.1109/TCBB.2004.2>.

Authors:Jos Hageman [aut, cre]

SIMPLICA_1.0.0.tar.gz
SIMPLICA_1.0.0.zip(r-4.7-any)SIMPLICA_1.0.0.zip(r-4.6-any)SIMPLICA_1.0.0.zip(r-4.5-any)
SIMPLICA_1.0.0.tgz(r-4.6-any)SIMPLICA_1.0.0.tgz(r-4.5-any)
SIMPLICA_1.0.0.tar.gz(r-4.7-any)SIMPLICA_1.0.0.tar.gz(r-4.6-any)
SIMPLICA_1.0.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
SIMPLICA/json (API)

# Install 'SIMPLICA' in R:

install.packages('SIMPLICA', repos = c('https://joshageman.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/joshageman/simplica/issues

Datasets:

simplicaToy - Toy matrix with one multiplicative and one additive bicluster

On CRAN:

3.18 score 3 stars 1 scripts 189 downloads 17 exports 25 dependencies

Last updated from:87cc15bac3. Checks:7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
linux-devel	NOTE	108
source / vignettes	OK	143
linux-release	NOTE	92
macos-release	NOTE	159
macos-oldrel	NOTE	193
windows-devel	NOTE	63
windows-release	NOTE	62
windows-oldrel	NOTE	56
wasm-release	OK	97

Exports:additiveMatrix additiveMatrixFitter componentCVPatterns defaultPatternFitters defaultPatternFunctions fitness fitnessForOneComponent gaintegerMutation gaintegerOnePointCrossover gaintegerPopulationFactory multiplicativeMatrix multiplicativeMatrixFitter plotComponentResult SCAMonitorFactory simplica simplicaCV summaryComponents

Dependencies:cli codetools cpp11 crayon farver foreach GA ggplot2 ggsci glue gtable isoband iterators labeling lifecycle R6 RColorBrewer Rcpp RcppArmadillo rlang S7 scales vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Generate an additive approximation of a data matrix	additiveMatrix
Additive Pattern Fitter	additiveMatrixFitter
Cross-Validation of Simplivariate Component Patterns	componentCVPatterns
Default Pattern Fitters for SIMPLICA	defaultPatternFitters
Default pattern generators for SIMPLICA	defaultPatternFunctions
Fitness function with automatic pattern selection per Simplivariate Component	fitness
Compute best pattern-based fitness for a single Simplivariate Component	fitnessForOneComponent
Integer mutation operator for genetic algorithms	gaintegerMutation
One-point crossover operator for integer-encoded genetic algorithms	gaintegerOnePointCrossover
GA Integer Population Factory	gaintegerPopulationFactory
Global Variables Declaration	globals
Generate an multiplicative approximation of a data matrix	multiplicativeMatrix
Multiplicative Pattern Fitter	multiplicativeMatrixFitter
Plot non-contiguous simplivariate components by pattern type, with optional reordering	plotComponentResult
Print method for summaryComponents	print.summaryComponents
Simplivariate Component Analysis monitoring function factory for GA progress	SCAMonitorFactory
SIMPLICA: Simultaneous Identification of Simplivariate Components	simplica
Test Simplivariate Components with Cross-Validation Pattern Selection	simplicaCV
Toy matrix with one multiplicative and one additive bicluster	simplicaToy
Summarize GA-found Simplivariate Components	summaryComponents