1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
|
## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
# Copyright (C) 2012 - 2021 Reza Mohammadi |
# |
# This file is part of BDgraph package. |
# |
# BDgraph is free software: you can redistribute it and/or modify it under |
# the terms of the GNU General Public License as published by the Free |
# Software Foundation; see <https://cran.r-project.org/web/licenses/GPL-3>.|
# |
# Maintainer: Reza Mohammadi <a.mohammadi@uva.nl> |
## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
# Non-parametric transfer function for non-normal data |
## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
bdgraph.npn = function( data, npn = "shrinkage", npn.thresh = NULL )
{
if( inherits( data, "sim" ) ) data <- data $ data
if( !is.matrix( data ) & !is.data.frame( data ) ) stop( "Data must be a matrix or dataframe" )
if( is.data.frame( data ) ) data = data.matrix( data )
if( any( is.na( data ) ) ) stop( "Data must contain no missing values" )
n <- nrow( data )
# - - - shrinkage transfer - - - - - - - - - - - - - - - - - - - - - - - - |
if( npn == "shrinkage" )
{
data = stats::qnorm( apply( data, 2, rank ) / ( n + 1 ) )
#data = data / stats::sd( data[ , 1 ] )
data = t( ( t( data ) - apply( data, 2, mean ) ) / apply( data, 2, stats::sd ) )
}
# - - - truncation transfer - - - - - - - - - - - - - - - - - - - - - - - -|
if( npn == "truncation" )
{
if( is.null( npn.thresh ) ) npn.thresh = 0.25 * ( n ^ ( -0.25 ) ) * ( pi * log( n ) ) ^ ( -0.5 )
data = stats::qnorm( pmin( pmax( apply( data, 2, rank ) / n, npn.thresh ), 1 - npn.thresh ) )
data = data / stats::sd( data[ , 1 ] )
}
# - - - skeptic transfer - - - - - - - - - - - - - - - - - - - - - - - - - |
if( npn == "skeptic" ) data = 2 * sin( pi / 6 * stats::cor( data, method = "spearman" ) )
return( data )
}
## - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - |
|
