fastTopics: Fast Algorithms for Fitting Topic Models and Non-Negative Matrix Factorizations to Count Data

Implements fast, scalable optimization algorithms for fitting topic models ("grade of membership" models) and non-negative matrix factorizations to count data. The methods exploit the special relationship between the multinomial topic model (also, "probabilistic latent semantic indexing") and Poisson non-negative matrix factorization. The package provides tools to compare, annotate and visualize model fits, including functions to efficiently create "structure plots" and identify key features in topics. The 'fastTopics' package is a successor to the 'CountClust' package. For more information, see <doi:10.48550/arXiv.2105.13440> and <doi:10.1186/s13059-023-03067-9>. Please also see the GitHub repository for additional vignettes not included in the package on CRAN.

Version:	0.6-192
Depends:	R (≥ 3.3.0)
Imports:	graphics, utils, methods, stats, Matrix, gtools, quadprog, irlba, dplyr, Rtsne, uwot, ashr, Rcpp (≥ 1.0.12), RcppParallel (≥ 5.1.7), RhpcBLASctl, parallel, progress, pbapply, ggplot2 (≥ 3.3.0), ggrepel (≥ 0.9.0), cowplot, plotly, htmlwidgets
LinkingTo:	Rcpp, RcppParallel, RcppArmadillo
Suggests:	Ternary, testthat, knitr, rmarkdown
Published:	2024-07-09
DOI:	10.32614/CRAN.package.fastTopics
Author:	Peter Carbonetto [aut, cre], Kevin Luo [aut], Kushal Dey [aut], Joyce Hsiao [ctb], Abhishek Sarkar [ctb], Anthony Hung [ctb], Xihui Lin [ctb], Paul C. Boutros [ctb], Minzhe Wang [ctb], Tracy Ke [ctb], Eric Weine [ctb], Matthew Stephens [aut]
Maintainer:	Peter Carbonetto <peter.carbonetto at gmail.com>
BugReports:	https://github.com/stephenslab/fastTopics/issues
License:	BSD_2_clause + file LICENSE
Copyright:	inst/COPYRIGHTS fastTopics copyright details
URL:	https://stephenslab.github.io/fastTopics/, https://github.com/stephenslab/fastTopics
NeedsCompilation:	yes
SystemRequirements:	GNU make
Citation:	fastTopics citation info
Materials:	README
CRAN checks:	fastTopics results

Documentation:

Reference manual:	fastTopics.pdf
Vignettes:	Relationship between NMF and topic modeling Topic modeling vs. clustering

Downloads:

Package source:	fastTopics_0.6-192.tar.gz
Windows binaries:	r-devel: fastTopics_0.6-192.zip, r-release: fastTopics_0.6-192.zip, r-oldrel: fastTopics_0.6-192.zip
macOS binaries:	r-release (arm64): fastTopics_0.6-192.tgz, r-oldrel (arm64): fastTopics_0.6-192.tgz, r-release (x86_64): fastTopics_0.6-192.tgz, r-oldrel (x86_64): fastTopics_0.6-192.tgz
Old sources:	fastTopics archive

Linking:

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