Package: FinfoMDS 1.3.0

Soobin Kim

FinfoMDS: Multidimensional Scaling with F-ratio for microbiome visualization

F-informed MDS is a new multidimensional scaling-based ordination method that configures data distribution based on the F-statistic (i.e., the ratio of dispersion between groups with shared or differing labels).

Authors:Soobin Kim [aut, cre], Hyungseok Kim [aut]

FinfoMDS_1.3.0.tar.gz
FinfoMDS_1.3.0.zip(r-4.7)FinfoMDS_1.3.0.zip(r-4.6)FinfoMDS_1.3.0.zip(r-4.5)
FinfoMDS_1.3.0.tgz(r-4.6-any)FinfoMDS_1.3.0.tgz(r-4.5-any)
FinfoMDS_1.3.0.tar.gz(r-4.7-any)FinfoMDS_1.3.0.tar.gz(r-4.6-any)
FinfoMDS_1.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FinfoMDS/json (API)

# Install 'FinfoMDS' in R:

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

Bug tracker:https://github.com/soob-kim/finfomds/issues

Datasets:

microbiome - Microbiome dataset

On BioConductor:FinfoMDS-1.3.0(bioc 3.24)FinfoMDS-1.2.0(bioc 3.23)

dimensionreduction multidimensionalscaling visualization microbiome

4.48 score 2 stars 2 scripts 190 downloads 7 exports 57 dependencies

Last updated from:ca0a81513d. Checks:1 WARNING, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	197
linux-devel-x86_64	OK	351
source / vignettes	OK	286
linux-release-x86_64	OK	346
macos-release-arm64	OK	153
macos-oldrel-arm64	OK	140
windows-devel	OK	212
windows-release	OK	203
windows-oldrel	OK	197
wasm-release	OK	146

Exports:fmds getDistMat getIndMat getP mdsObj pairByRank pseudoF

Dependencies:ade4 ape Biobase BiocGenerics biomformat Biostrings cli cluster codetools cpp11 crayon data.table digest farver foreach generics ggplot2 glue gtable igraph IRanges isoband iterators jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv multtest nlme permute phyloseq pixmap pkgconfig plyr R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang S4Vectors S7 scales Seqinfo sp stringi stringr survival vctrs vegan viridisLite withr XVector

FinfoMDS: Multidimensional scaling informed by F-statistic

Rendered fromFinfoMDS.Rmdusingknitr::rmarkdown

Last update: 2025-09-03
Started: 2025-05-21

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
FMDS calculation using MM algorithm	fmds
Distance between vectors	getDistMat
Get index matrix	getIndMat
Compute p-value from PERMANOVA test	getP
Objective term of MDS	mdsObj
Microbiome dataset	microbiome
Get p-value matrix	pairByRank
Compute pseudo-F statistic for PERMANOVA	pseudoF