rnetSubset-class

rnetSubset

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

rnetSubset-class function

<dl class="dl-horizontal">
<dt><code>subset</code></dt><dd>The expression used to define the stratum of data represented by the rnet, e.g., if Statra_def = as.expression(Year == 2008), the rnet is estimated from the subset of data collected in the Year 2008.</dd>
</dl>

Slots

An S4 class containing the information of an rnet representing one stratum of data. These objects are used to handle rnet objects and need not be called by the user. — rnetSubset-class

An S4 class containing the information of an rnet representing one stratum of data. These objects are used to handle rnet objects and need not be called by the user.

rnetSubset-class: An S4 class containing the information of an rnet representing one stratum of data. These objects are used to handle rnet objects and need not be called by the user.

Description

Arguments

Slots