dimRed (version 0.0.3)

embed: dispatches the different methods for dimensionality reduction

Description

wraps around all dimensionality reduction functions.

Usage

embed(.data, ...)
"embed"(.formula, .data, .method = dimRedMethodList(), .mute = character(0), .keep.org.data = TRUE, ...)
"embed"(.data, .method = dimRedMethodList(), .mute = character(0), .keep.org.data = TRUE, ...)
"embed"(.data, .method = dimRedMethodList(), .mute = character(0), .keep.org.data = TRUE, ...)

Arguments

.data

object of class dimRedData

...

the pameters, internally passed as a list to the dimensionality reduction method as pars = list(...)

.formula

a formula, see as.dimRedData.

.method

character vector naming one of the dimensionality reduction techniques.

.mute

a character vector containing the elements you want to mute (c("message", "output")), defaults to character(0).

.keep.org.data

TRUE/FALSE keep the original data.

Value

an object of class dimRedResult

Methods (by class)

• formula: embed a data.frame using a formula.
• ANY: Embed anything as long as it can be coerced to dimRedData.
• dimRedData: Embed a dimRedData object

Details

Method must be one of dimRedMethodList(), partial matching is performed. All parameters start with a dot, to avoid clashes with partial argument matching (see the R manual section 4.3.2), if there should ever occur any clashes in the arguments, call the function with all arguments named, e.g. embed(.data = dat, .method = "mymethod", .d = "some parameter").

Examples

## Not run: 
# embed_methods <- dimRedMethodList()
# quality_methods <- dimRedQualityList()
# dataset <- loadDataSet("Iris")
# 
# quality_results <- matrix(NA, length(embed_methods), length(quality_methods),
#                               dimnames = list(embed_methods, quality_methods))
# embedded_data <- list()
# 
# for (e in embed_methods) {
#   message("embedding: ", e)
#   embedded_data[[e]] <- embed(dataset, e, .mute = c("message", "output"))
#   for (q in quality_methods) {
#     message("  quality: ", q)
#     quality_results[e, q] <- tryCatch(
#       quality(embedded_data[[e]], q),
#       error = function(e) NA
#     )
#   }
# }
# 
# print(quality_results)
# ## End(Not run)
## embed a data.frame using a formula:
head(as.data.frame(
  embed(Species ~ Sepal.Length + Sepal.Width + Petal.Length + Petal.Width,
        iris, "PCA")
))

head(as.data.frame(
  embed(iris[, 1:4], "PCA")
))
head(as.data.frame(
  embed(as.matrix(iris[, 1:4]), "PCA")
))