NetworkToolbox (version 1.2.2)

bootgen: Bootstrapped Network Generalization

Description

Bootstraps the sample to identify the most stable correlations. Also produces a network that is penalizes low reliability edges. This function is useful for overcoming the structural constraint of the IFN approach. STILL BEING DEVELOPED

Usage

bootgen(data, method = c("MaST", "TMFG", "LoGo", "threshold"),
  n = nrow(data), iter = 1000, normal = FALSE,
  na.data = c("pairwise", "listwise", "fiml", "none"), cores, ...)

Arguments

data

A set of data

method

A network filtering method. Defaults to "TMFG"

n

Number of people to use in the bootstrap. Defaults to full sample size

iter

Number of bootstrap iterations. Defaults to 1000 iterations

normal

Should data be transformed to a normal distribution? Defaults to FALSE. Data is not transformed to be normal. Set to TRUE if data should be transformed to be normal (computes correlations using the cor_auto function)

na.data

How should missing data be handled? For "listwise" deletion the na.omit function is applied. Set to "fiml" for Full Information Maxmimum Likelihood (corFiml). Full Information Maxmimum Likelihood is recommended but time consuming

cores

Number of computer processing cores to use for bootstrapping samples. Defaults to n - 1 total number of cores. Set to any number between 1 and maxmimum amount of cores on your computer

...

Additional arguments for filtering methods

Value

Returns a list that includes:

orignet

the original filtered network

bootmat

correlation matrix of the mean bootstrapped network

netrel

unfiltered reliabilities of all of the connections

References

Musciotto, F., Marotta, L., Micciche, S., & Mantegna, R. N. (2018). Bootstrap validation of links of a minimum spanning tree. arXiv, 1802.03395. doi: 1802.03395

Tumminello, M., Coronnello, C., Lillo, F., Micciche, S., & Mantegna, R. N. (2007). Spanning trees and bootstrap reliability estimation in correlation-based networks. International Journal of Bifurcation and Chaos, 17, 2319-2329. doi: 10.1142/S0218127407018415

Examples

# NOT RUN {
bootTMFG<-bootgen(neoOpen)

bootLoGo<-bootgen(neoOpen,method="LoGo")

bootMaST<-bootgen(neoOpen,method="MaST")

bootThreshold<-bootgen(neoOpen,method="threshold")
# }
# NOT RUN {
# }