EC_COORDS

A set of x-y coordinates for drawing an R-net for the example E. coli data.

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>.

William Love

Rnets

Resistance Relationship Networks using Graphical LASSO

EC_COORDS function

A dataframe containing coordinates for vertex locations when plotting networks<dl class="dl-horizontal">
 <dt>vert</dt><dd>The 3 letter code corresponding to V_ATTRS$Code</dd>
 <dt>x</dt><dd>x-coordinate for positioning vertex in plot</dd>
 <dt>y</dt><dd>x-coordinate for positioning vertex in plot</dd>
</dl>

Format

Example Vertex coordinates — EC_COORDS

A dataframe containing coordinates for vertex locations when plotting networks<dl class='dl-horizontal'>
 <dt>vert</dt><dd>The 3 letter code corresponding to V_ATTRS$Code</dd>
 <dt>x</dt><dd>x-coordinate for positioning vertex in plot</dd>
 <dt>y</dt><dd>x-coordinate for positioning vertex in plot</dd>
</dl>

EC_COORDS: Example Vertex coordinates

Description

Usage

Arguments

Format