do.idmap: Interactive Document Map

Description

Interactive Document Map originates from text analysis to generate maps of documents by placing similar documents in the same neighborhood. After defining pairwise distance with cosine similarity, authors asserted to use either NNP or FastMap as an engine behind.

Usage

do.idmap(
  X,
  ndim = 2,
  preprocess = c("null", "center", "scale", "cscale", "whiten", "decorrelate"),
  engine = c("NNP", "FastMap")
)

Value

a named list containing

Y: an \((n\times ndim)\) matrix whose rows are embedded observations.
trfinfo: a list containing information for out-of-sample prediction.

Arguments

X: an \((n\times p)\) matrix or data frame whose rows are observations and columns represent independent variables.
ndim: an integer-valued target dimension.
preprocess: an additional option for preprocessing the data. Default is "null". See also aux.preprocess for more details.
engine: either NNP or FastMap.

References

minghim_contentbased_2006Rdimtools

Examples

Run this code

# \donttest{
## load iris data
data(iris)
set.seed(100)
subid = sample(1:150,50)
X     = as.matrix(iris[subid,1:4])
lab   = as.factor(iris[subid,5])

## let's compare with other methods
out1 <- do.pca(X, ndim=2)
out2 <- do.lda(X, ndim=2, label=lab)
out3 <- do.idmap(X, ndim=2, engine="NNP")

## visualize
opar <- par(no.readonly=TRUE)
par(mfrow=c(1,3))
plot(out1$Y, pch=19, col=lab, main="PCA")
plot(out2$Y, pch=19, col=lab, main="LDA")
plot(out3$Y, pch=19, col=lab, main="IDMAP")
par(opar)
# }