added information to supercede dualTotalCor and Oinformation

hfgolino · Aug 4, 2024 · a49061f · a49061f
1 parent a43cd4d
commit a49061f
Show file tree

Hide file tree

Showing 10 changed files with 378 additions and 335 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: EGAnet
 Title: Exploratory Graph Analysis – a Framework for Estimating the Number of Dimensions in Multivariate Data using Network Psychometrics
 Version: 2.0.7
-Date: 2024-08-03
+Date: 2024-08-04
 Authors@R: c(person("Hudson", "Golino", email = "hfg9s@virginia.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-1601-1447")),
 	     person("Alexander", "Christensen", email = "alexpaulchristensen@gmail.com", role = "aut", comment = c(ORCID = "0000-0002-9798-7037")),
 	     person("Robert", "Moulder", email = "rgm4fd@virginia.edu", role = "ctb", comment = c(ORCID = "0000-0001-7504-9560")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -69,7 +69,6 @@ export(EGA.estimate)
 export(EGA.fit)
 export(Embed)
 export(LCT)
-export(Oinformation)
 export(TMFG)
 export(UVA)
 export(auto.correlate)
@@ -85,7 +84,6 @@ export(compare.EGA.plots)
 export(convert2igraph)
 export(convert2tidygraph)
 export(dimensionStability)
-export(dualTotalCor)
 export(dynEGA)
 export(dynEGA.ind.pop)
 export(entropyFit)
@@ -96,6 +94,7 @@ export(glla)
 export(hierEGA)
 export(igraph2matrix)
 export(infoCluster)
+export(information)
 export(invariance)
 export(itemStability)
 export(jsd)

diff --git a/NEWS b/NEWS
@@ -8,7 +8,7 @@ WEBSITE: https://r-ega.net
 
 + ADD: `network.compare` function to test for differences in network structures using three different metrics (Frobenius Norm, Jensen-Shannon Similarity, total network strength)
 
-+ ADD: information theoretic measures of dual total correlation (`dualTotalCor`) and O-information (`Oinformation`)
++ ADD: a general function called `information` to compute several information theory measures
 
 + UPDATE: added 'signed' argument in `jsd` to allow for signed or absolute networks to be used in computations (includes downstream functions: `infoCluster`)
 

diff --git a/R/Oinformation.R b/R/Oinformation.R
diff --git a/R/dualTotalCor.R b/R/dualTotalCor.R
diff --git a/R/helpers.R b/R/helpers.R
@@ -3231,15 +3231,6 @@ matrix_entropy <- function(density_matrix, base = 2.718282)
 
 }
 
-#' @noRd
-# Basic entropy calculation ----
-# Returns entropy value
-# Updated 29.06.2023
-entropy <- function(values, base = 2.718282)
-{
-  return(-sum(values * log(values, base = base), na.rm = TRUE))
-}
-
 #' @noRd
 # Positive definite matrix ----
 # Logical for whether a matrix is positive definite