| register_smacof {seriation} | R Documentation |
Register Seriation Methods from Package smacof
Description
Registers the "MDS_smacof" method for seriate() based on multidimensional
scaling using stress majorization and the corresponding "smacof_stress0"
criterion implemented in package smacof (de Leeuw & Mair, 2009).
Usage
register_smacof()
Details
Seriation method "smacof" implements stress majorization with several transformation functions.
These functions are passed on as the type control parameter. We default
to "ratio", which together with "interval" performs metric MDS.
"ordinal" can be used
for non-metric MDS. See smacof::smacofSym() for details on the
control parameters.
The corresponding criterion called "smacof_stress0" is also registered.
There additional parameter type is used to specify the used
transformation function. It should agree with the function used for seriation.
See smacof::stress0() for details on the stress calculation.
Note: Package smacof needs to be installed.
Value
Nothing.
References
Jan de Leeuw, Patrick Mair (2009). Multidimensional Scaling Using Majorization: SMACOF in R. Journal of Statistical Software, 31(3), 1-30. doi:10.18637/jss.v031.i03
See Also
Other seriation:
register_DendSer(),
register_GA(),
register_optics(),
register_tsne(),
register_umap(),
registry_for_seriaiton_methods,
seriate(),
seriate_best()
Examples
## Not run:
register_smacof()
get_seriation_method("dist", "MDS_smacof")
d <- dist(random.robinson(20, pre = TRUE))
## use Banded AR form with default clustering (complete-link)
o <- seriate(d, "MDS_smacof", verbose = TRUE)
pimage(d, o)
# recalculate stress for the order
MDS_stress(d, o)
# ordinal MDS. stress needs to be calculated using the correct type with stress0
o <- seriate(d, "MDS_smacof", type = "ordinal", verbose = TRUE)
criterion(d, o, method = "smacof_stress0", type = "ordinal")
## End(Not run)