This package was removed from CRAN on 2020-03-07. Its history is shown below.

Reason: check problems were not corrected despite reminders

Details below reflect version 1.2.1, its last release before removal.

Rnets

1.2.1

Resistance Relationship Networks using Graphical LASSO

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by William Love3 releasesCRAN page ↗

Novel methods are needed to analyze the large amounts of antimicrobial resistance (AMR) data generated by AMR surveillance programs. This package is used to estimate resistance relationship networks, or 'Rnets', from empirical antimicrobial susceptibility data. These networks can be used to study relationships between antimicrobial resistances (typically measured using MICs) and genes in populations. The 'GitHub' for this package is available at https://GitHub.com/EpidemiologyDVM/Rnets. Bug reports and features requests should be directed to the same 'GitHub' site. The methods used in 'Rnets' are available in the following publications: An overview of the method in WJ Love, et al., "Markov Networks of Collateral Resistance: National Antimicrobial Resistance Monitoring System Surveillance Results from Escherichia coli Isolates, 2004-2012" (2016) doi:10.1371/journal.pcbi.1005160; The graphical LASSO for sparsity in J Friedman, T Hastie, R Tibshirani "Sparse inverse covariance estimation with the graphical lasso" (2007) doi:10.1093/biostatistics/kxm045; L1 penalty selection in H Liu, K Roeder, L Wasserman "Stability Approach to Regularization Selection (StARS) for High Dimensional Graphical Models" (2010) arXiv:1006.3316; Modularity for graphs with negative edge weights in S Gomez, P Jensen, A Arenas. "Analysis of community structure in networks of correlated data" (2009) doi:10.1103/PhysRevE.80.016114.

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/Rnets/Rnets_1.2.1.tar.gz"
pkgFile <- "Rnets_1.2.1.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 (1.2.1) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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

READMEYes · 575 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 78%
Documented parameters: 96%
Return-value docs: 91%
References docs: 0%

Downloads

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Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (5)

R >= 3.1.2glasso igraph data.table(>= 1.9.6)stringr

Imports (3)

methodsICSNP rlang

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

William Love

Author, Maintainer

Authors (1)

William Love

Author, Maintainer

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.0.0 released · 2020-04-24
archivedRemoved from CRAN
2020-03-07
check problems were not corrected despite reminders
1.2.1
2019-07-23 · diff ↗
R
R 3.6.0 released · 2019-04-26
1.0.2
2018-09-11 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.9.8
2017-12-12
R
R 3.4.0 released · 2017-04-21

Package metadata

Total releases: 3
License: GPL-3 OSI
Minimum R: ≥ 3.1.2
Bundled data: 93 KB / 4 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

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