rnetStrata-class

rnetStrata

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

rnetStrata-class function

<dl class="dl-horizontal">
<dt><code>stratify_by</code></dt><dd>The name of the variable used to the original data, e.g. if Stratify_by = 'Year', the object contains 1 rnetSubset object for each unique value of the variable "year" in the dataset.</dd></dl><dt><code>E_aggr</code></dt><dd>A matrix containing every edge found in the entire set of rnets, and the stratum in which it was found.</dd><dt><code>R_set</code></dt><dd>A list of rnetStrata objects for each strata of the declared Stratify_by variable.</dd>

Slots

An S4 class containing multiple Rnets, each 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. — rnetStrata-class

An S4 class containing multiple Rnets, each 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.

rnetStrata-class: An S4 class containing multiple Rnets, each 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