dispatches the different methods for dimensionality reduction
wraps around all dimensionality reduction functions.
embed(.data, ...) ## S4 method for signature 'formula' embed(.formula, .data, .method = dimRedMethodList(), .mute = character(0), .keep.org.data = TRUE, ...) ## S4 method for signature 'ANY' embed(.data, .method = dimRedMethodList(), .mute = character(0), .keep.org.data = TRUE, ...) ## S4 method for signature 'dimRedData' embed(.data, .method = dimRedMethodList(), .mute = character(0), .keep.org.data = TRUE, ...)
.data |
object of class |
... |
the parameters, internally passed as a list to the dimensionality
reduction method as |
.formula |
a formula, see |
.method |
character vector naming one of the dimensionality reduction techniques. |
.mute |
a character vector containing the elements you want to mute
( |
.keep.org.data |
|
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")
.
an object of class dimRedResult
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
## embed a data.frame using a formula: as.data.frame( embed(Species ~ Sepal.Length + Sepal.Width + Petal.Length + Petal.Width, iris, "PCA") ) ## embed a data.frame and return a data.frame as.data.frame(embed(iris[, 1:4], "PCA")) ## embed a matrix and return a data.frame as.data.frame(embed(as.matrix(iris[, 1:4]), "PCA")) ## Not run: ## embed dimRedData objects 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)
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