Rdimtools (version 1.0.6)

do.pflpp: Parameter-Free Locality Preserving Projection

Description

Conventional LPP is known to suffer from sensitivity upon choice of parameters, especially in building neighborhood information. Parameter-Free LPP (PFLPP) takes an alternative step to use normalized Pearson correlation, taking an average of such similarity as a threshold to decide which points are neighbors of a given datum.

Usage

do.pflpp(
  X,
  ndim = 2,
  preprocess = c("center", "scale", "cscale", "whiten", "decorrelate")
)

Arguments

X

an \((n\times p)\) matrix or data frame whose rows are observations

ndim

an integer-valued target dimension.

preprocess

an additional option for preprocessing the data. Default is "center". See also aux.preprocess for more details.

Value

a named list containing

Y

an \((n\times ndim)\) matrix whose rows are embedded observations.

projection

a \((p\times ndim)\) whose columns are basis for projection.

trfinfo

a list containing information for out-of-sample prediction.

References

dornaika_enhanced_2013Rdimtools

Examples

# NOT RUN {
## use iris data
data(iris)
set.seed(100)
subid = sample(1:150, 50)
X     = as.matrix(iris[subid,1:4])
label = as.factor(iris[subid,5])

## compare with PCA
out1 = do.pca(X, ndim=2)
out2 = do.pflpp(X, ndim=2)

## visualize
opar <- par(no.readonly=TRUE)
par(mfrow=c(1,2))
plot(out1$Y, pch=19, col=label, main="PCA")
plot(out2$Y, pch=19, col=label, main="Parameter-Free LPP")
par(opar)

# }