This package was removed from CRAN on 2023-04-27. Its history is shown below.

Reason: : this package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/microSTASIS.html>

Details below reflect version 0.1.0, its last release before removal.

microSTASIS

0.1.0

Microbiota STability ASsessment via Iterative cluStering

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Pedro Sánchez-Sánchez1 releasesCRAN page ↗

The toolkit 'µSTASIS' has been developed for the stability analysis of microbiota in a temporal framework by leveraging on iterative clustering. Concretely, the core function uses Hartigan-Wong k-means algorithm as many times as possible for stressing out paired samples from the same individuals to test if they remain together for multiple numbers of clusters over a whole data set of individuals. Moreover, the package includes multiple functions to subset samples from paired times, validate the results or visualize the output.

Install

BioconductorR (source archive)Ubuntu (r2u)openSUSE (OBS)

BiocManager::install("microSTASIS")

Installs the current Bioconductor release. Requires the BiocManager package.

url <- "https://cran.r-project.org/src/contrib/Archive/microSTASIS/microSTASIS_0.1.0.tar.gz"
pkgFile <- "microSTASIS_0.1.0.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.1.0) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-microstasis

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-microSTASIS

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 83%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on66 r2u38 autocran456 bioconda

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (10)

crayon fmsb future future.apply ggplot2 ggside progressr reshape2statsstringr

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

R 715 (61%)Rd 462 (39%)

Code characteristics

Cyclomatic complexity: 4.0 median / 9 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

12 12 exported

Complexity

4.9 avg / 9 max

Call network

12 nodes / 0 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (2)

Maintainer (1)

Pedro Sánchez-Sánchez

Author, Maintainer

Authors (2)

Pedro Sánchez-Sánchez

Author, Maintainer

Alfonso Benítez-Páez

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-04-27
: this package is now available from Bioconductor only, see <https://www.bioconductor.org/packages/release/bioc/html/microSTASIS.html>
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.0
2021-09-14
R
R 4.1.0 released · 2021-05-18

Package metadata

Total releases: 1
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 86 KB / 1 file
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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