parafac4microbiome: Parallel Factor Analysis Modelling of Longitudinal Microbiome Data
Creation and selection of PARAllel FACtor Analysis (PARAFAC) models of longitudinal microbiome data. You can import your own data with our import functions or use one of the example datasets to create your own PARAFAC models. Selection of the optimal number of components can be done using assessModelQuality() and assessModelStability(). The selected model can then be plotted using plotPARAFACmodel(). The Parallel Factor Analysis method was originally described by Caroll and Chang (1970) <doi:10.1007/BF02310791> and Harshman (1970) <https://www.psychology.uwo.ca/faculty/harshman/wpppfac0.pdf>.
| Version: | 1.0.3 |
| Depends: | R (≥ 2.10) |
| Imports: | compositions, cowplot, doParallel, dplyr, foreach, ggplot2, ggpubr, lifecycle, magrittr, methods, mize, multiway, parallel, pracma, rlang, rTensor, stats, tidyr |
| Suggests: | knitr, MicrobiotaProcess, phyloseq, rmarkdown, SummarizedExperiment, testthat (≥ 3.0.0), TreeSummarizedExperiment, withr |
| Published: | 2024-09-24 |
| DOI: | 10.32614/CRAN.package.parafac4microbiome |
| Author: | Geert Roelof van der Ploeg
 [aut, cre],
Johan Westerhuis
[ctb],
Anna Heintz-Buschart
[ctb],
Age Smilde [ctb],
University of Amsterdam [cph, fnd] |
| Maintainer: | Geert Roelof van der Ploeg <g.r.ploeg at uva.nl> |
| BugReports: | https://github.com/GRvanderPloeg/parafac4microbiome/issues |
| License: | MIT + file LICENSE |
| URL: | https://grvanderploeg.github.io/parafac4microbiome/, https://github.com/GRvanderPloeg/parafac4microbiome |
| NeedsCompilation: | no |
| Materials: | README NEWS |
| CRAN checks: | parafac4microbiome results |
Documentation:
| Reference manual: | parafac4microbiome.pdf |
| Vignettes: |
Fujita2023_analysis (source, R code) PARAFAC_introduction (source, R code) Shao2019_analysis (source, R code) vanderPloeg2024_analysis (source, R code) |
Downloads:
| Package source: | parafac4microbiome_1.0.3.tar.gz |
| Windows binaries: | r-devel: parafac4microbiome_1.0.3.zip, r-release: parafac4microbiome_1.0.3.zip, r-oldrel: parafac4microbiome_1.0.3.zip |
| macOS binaries: | r-release (arm64): parafac4microbiome_1.0.3.tgz, r-oldrel (arm64): parafac4microbiome_1.0.3.tgz, r-release (x86_64): parafac4microbiome_1.0.3.tgz, r-oldrel (x86_64): parafac4microbiome_1.0.3.tgz |
| Old sources: | parafac4microbiome archive |
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