See "L1_selection" documentation for more information.

`RawData`

A dataframe containing the original dataset.

`cor_method`

The type of correlation matrix to use. Must be a partial match to one of the following strings: 'pearson', 'spearman', 'kendall'.

`cor_pairing`

Method for handling how missing data is handled in pairs. See 'pair' argument in function 'cor' for more information.

`n_threshold`

The minimum number of valid pair-wise observations that must exist for an edge to be estimated. Vertex pairs with fewer valid pair-wise observations are assumed to be conditiontally independent.

`L1_orig`

The declared L1 penalty to be used when estimating rnet topology

`v_set_orig`

The declared set of k variables to be included in the rnet as vertices

`Forced_zeros`

A matrix with 2 columns containing pairs of vertices to force to be conditionally independent in the rnet

`Layout_master`

A k x 2 matrix x & y coordinates of each vertex in the graph.

`Data`

A dataframe containing the dataset

`L1_set`

a numeric vector containing the candidate L1 penalties

`B`

The number of subsamples to draw from the data to evaluate topologic stability

`B_method`

Assigned either "proportionate" or "Total number" depending on how subsample size is determined.

`B_sets`

A matrix (n_B x B) containing the rownumbers of the subsamples

`Data_b`

An arrary (n_b x k x B) containing the data from the B_sets matrix

`pr_b`

The size of the subsample B as a proportion of the complete dataset

`n_b`

The size of the subsample

`W_aggr`

An array (k x k x B x L1) containg all the weighted adjacency matrices generated by the all of subsamples over the L1 penalties

`A_aggr`

An array (k x k x B x L1) containg all the adjacency matrices generated by the all of subsamples over the L1 penalties

`M`

A dataframe with with graphical density data over the set of generated networks.

`Edge_stability`

A dataframe showing edge stability over the set of generated networks.

`StARS_D`

A vector of D_b values used for L1 selection.

EpidemiologyDVM/Rnets documentation built on Dec. 8, 2017, 12:27 a.m.

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