BDgraph (version 2.25)

compare: Comparing the results

Description

With this function, we can check the performance of our methods and compare it with other alternative approaches.

Usage

compare( sim.obj, bdgraph.obj, bdgraph.obj2 = NULL, bdgraph.obj3 = NULL, 
          colnames = NULL, vis = FALSE )

Arguments

sim.obj

An object with S3 class "sim" from function bdgraph.sim. It also can be the adjacency matrix corresponding to the true graph structure.

bdgraph.obj

An object with S3 class "bdgraph" from function bdgraph. It also can be an adjacency matrix corresponding to an estimated graph.

bdgraph.obj2

An object with S3 class "bdgraph" from function bdgraph. It also can be an adjacency matrix corresponding to an estimated graph. It is for comparing two different approaches.

bdgraph.obj3

An object with S3 class "bdgraph" from function bdgraph. It also can be an adjacency matrix corresponding to an estimated graph. It is for comparing three different approaches.

colnames

A character vector giving the column names for the result table.

vis

Visualize the true graph and estimated graph structures. The default is FALSE.

Value

• True positive
  The number of correctly estimated links.
• True negative
  The number of true non-existing links which is correctly estimated.
• False positive
  The number of links which they are not in the true graph, but are incorrectly estimated.
• False negative
  The number of links which they are in the true graph, but are not estimated.
• Accuracy
  the number of true results (both true positives and true negatives) divided by the total number of true and false results.
• Balanced F-score
  A weighted average of the "positive predictive" and "true positive rate". F-score value reaches its best value at 1 and worst score at 0.
• Positive predictive
  The number of correctly estimated links divided by the total number of links in the estimated graph.
• True positive rate
  The number of correctly estimated links divided by the total number of links in the true graph.
• False positive rate
  The false positive value divided by the total number of links in the true graph.

References

Mohammadi, A. and E. Wit (2015). Bayesian Structure Learning in Sparse Gaussian Graphical Models, Bayesian Analysis, 10(1):109-138 Mohammadi, A. and E. Wit (2015). BDgraph: An R Package for Bayesian Structure Learning in Graphical Models, arXiv:1501.05108 Mohammadi, A., F. Abegaz Yazew, E. van den Heuvel, and E. Wit (2015). Bayesian Gaussian Copula Graphical Modeling for Dupuytren Disease, arXiv:1501.04849

See Also

bdgraph and select

Examples

# Generating multivariate normal data from a 'random' graph
data.sim <- bdgraph.sim( n = 50, p = 6, size = 7, vis = TRUE )
    
# Running sampling algorithm based on GGMs 
sample.ggm <- bdgraph( data = data.sim, method = "ggm", iter = 10000 )
# Comparing the results
compare( data.sim, sample.ggm, colnames = c( "True graph", "GGM" ), vis = TRUE )
    
# Running sampling algorithm based on GCGMs
sample.gcgm <- bdgraph( data = data.sim, method = "gcgm", iter = 10000 )
# Comparing GGM and GCGM methods
compare( data.sim, sample.ggm, sample.gcgm, colnames = c("True graph", "GGM", "GCGM"), vis = TRUE )