| snha-package {snha} | R Documentation |
snha package - association chain graphs from correlation networks
Description
The snha package can be used to construct association chain graphs based on the St. Nicolas House Analysis (SNHA) algorithm as described in Groth et. al. 2019. and Hermanussen et. al. 2021.
Details
The package provides the following functions: Function for graph generation from data:
- snha(data)
applys the SNHA method on the data and returns a new snha graph object
S3 methods for snha graphs:
- plot.snha(x)
plots a snha graph
- as.list.snha(x)
return a list representation of a snha graph object
Utility functions:
- snha_get_chains(g)
returns the chains found by the algorithm as matrix
- snha_graph2data(A)
create for the given adjacency matrix some data with the appropiate correlations
- snha_layout(g)
calculate layout coordinates for the given graph or adjacency matrix
- snha_ll(g,chain)
calculate log-likelihood for the given chain of the snha graph
- snha_rsquare(data,g)
for given data and graph or adjacency matrix calculate linear model r-square value
Value
No return value
Author(s)
Detlef Groth <dgroth@uni-potsdam.de>
References
Groth, D., Scheffler, C., & Hermanussen, M. (2019). Body height in stunted Indonesian children depends directly on parental education and not via a nutrition mediated pathway - Evidence from tracing association chains by St. Nicolas House Analysis. Anthropologischer Anzeiger, 76 No. 5 (2019), p. 445 - 451. doi: 10.1127/anthranz/2019/1027
Hermanussen, M., Assmann, & Groth, D. (2021). Chain Reversion for Detecting Associations in Interacting Variables - St. Nicolas House Analysis. International Journal of Environmental Research and Public Health. 18, 4 (2021). doi: 10.3390/ijerph18041741.
Novine, M., Mattsson, C. C., & Groth, D. (2021). Network reconstruction based on synthetic data generated by a Monte Carlo approach. Human Biology and Public Health, 3:26. doi: 10.52905/hbph2021.3.26
Examples
library(MASS)
data(birthwt)
as=snha(birthwt[,-1])
plot(as)
as$theta
ls(as)
data(decathlon88)
head(decathlon88)
dec=snha(decathlon88,method="spearman",alpha=0.1)
plot(dec,layout='sam')