Resistance Relationship Networks using Graphical LASSO


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Documentation for package ‘Rnets’ version 1.0.2

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.Assign_Layout_Matrix Hidden function for assigning layout matrix
.Gen_R .Gen_R - internal methods for generating Rnets.
.Gen_R-method .Gen_R - internal methods for generating Rnets.
Assign_Emetadata Assign_Emetadata - Methods for assigning network edge metadata
Assign_Emetadata-method Assign_Emetadata - Methods for assigning network edge metadata
Assign_Vmetadata Assign_Vmetadata - Methods for assigning network vertex metadata
Assign_Vmetadata-method Assign_Vmetadata - Methods for assigning network vertex metadata
Clean_Sigma Clean_Sigma function
EC_COORDS Example Vertex coordinates
Estimate_pCorrs Estimation of partial correlation matrix from precision matrix
E_ATTRS Sample Edge Attributes
image image() method for plotting Rnet heatmaps
image.edge_heatmap image() method for plotting Rnet heatmaps
L1Selection L1 Selection for Rnets
NARMS_EC_DATA E. coli Isolate information from Nat'l Antimicrobial Resistance Monitoring System.
plot Plot methods for R-nets
plot-method Plot methods for R-nets
print-method Print methods of rnet objects.
Rnet R-net Methods
Rnet-method R-net Methods
rnet.L1.set An S4 class for accepting input data common for generating all rnet objects. These objects are used to handle rnet objects and need not be called by the user.
rnet.L1.set-class An S4 class for accepting input data common for generating all rnet objects. These objects are used to handle rnet objects and need not be called by the user.
rnetBasic An S4 class containg the information of a basic rnet. These objects are used to handle rnet objects and need not be called by the user.
rnetBasic-class An S4 class containg the information of a basic rnet. These objects are used to handle rnet objects and need not be called by the user.
rnetInput An S4 class for accepting input data common for generating all rnet objects. These objects are used to handle rnet objects and need not be called by the user.
rnetInput-class An S4 class for accepting input data common for generating all rnet objects. These objects are used to handle rnet objects and need not be called by the user.
rnetStrata 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.
rnetSubset 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.
Rnet_Heatmap Rnet_Heatmap - Function to generate a bitmap figure to represent edges in similar networks over time.
signed_modularity Robust Estimator of modularity (Gomez, et al 2009)
signed_modularity-method signed_modularity-igraph
signed_modularity-method signed_modularity-matrix
signed_modularity-method signed_modularity-rnetBasic
signed_modularity-method signed_modularity-rnetMultiStrata
Sq2Long Matrix reshaping function
summary Summary - rnetBasic
summary-method Summary - L1 selection object
summary-method Summary - rnetBasic
summary-method Summary - rnetStrata
summary-method Summary - rnetSubset
V_ATTRS Sample Vertex Attributes for NARMS_EC_DATA