A Framework for Dimensionality Reduction

---

Documentation for package ‘dimRed’ version 0.2.6

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

A C D E F G H I K L M N P Q R T U misc

dimRed-package

The dimRed package

-- A --

as.data.frame	Converts to data.frame
as.data.frame-method	Class "dimRedData"
as.data.frame-method	Class "dimRedResult"
as.dimRedData	Converts to dimRedData
as.dimRedData-method	Converts to dimRedData
AUC_lnK_R_NX	Method AUC_lnK_R_NX
AUC_lnK_R_NX-method	Method AUC_lnK_R_NX
AutoEncoder	AutoEncoder
AutoEncoder-class	AutoEncoder

-- C --

cophenetic_correlation	Method cophenetic_correlation
cophenetic_correlation-method	Method cophenetic_correlation

-- D --

dataSetList	Example Data Sets for dimensionality reduction
dataSets	Example Data Sets for dimensionality reduction
DiffusionMaps	Diffusion Maps
DiffusionMaps-class	Diffusion Maps
dimRed	The dimRed package
dimRedData	Class "dimRedData"
dimRedData-class	Class "dimRedData"
dimRedMethod-class	Class "dimRedMethod"
dimRedMethodList	dimRedMethodList
dimRedQualityList	Quality Criteria for dimensionality reduction.
dimRedResult	Class "dimRedResult"
dimRedResult-class	Class "dimRedResult"
distance_correlation	Method distance_correlation
distance_correlation-method	Method distance_correlation
DrL	Distributed Recursive Graph Layout
DrL-class	Distributed Recursive Graph Layout
DRR	Dimensionality Reduction via Regression
DRR-class	Dimensionality Reduction via Regression

-- E --

embed	dispatches the different methods for dimensionality reduction
embed-method	dispatches the different methods for dimensionality reduction

-- F --

FastICA	Independent Component Analysis
FastICA-class	Independent Component Analysis
FruchtermanReingold	Fruchterman Reingold Graph Layout
FruchtermanReingold-class	Fruchterman Reingold Graph Layout

-- G --

getData	Method getData
getData-method	Class "dimRedData"
getDimRedData	Method getDimRedData
getDimRedData-method	Class "dimRedResult"
getMeta	Method getMeta
getMeta-method	Class "dimRedData"
getNDim	Method getNDim
getNDim-method	Class "dimRedResult"
getOrgData	Method getOrgData
getOrgData-method	Class "dimRedResult"
getOtherData	Method getOtherData
getOtherData-method	Class "dimRedResult"
getPars	Method getPars
getPars-method	Class "dimRedResult"
getRotationMatrix	getRotationMatrix

-- H --

HLLE	Hessian Locally Linear Embedding
HLLE-class	Hessian Locally Linear Embedding

-- I --

installSuggests	getSuggests
inverse	Class "dimRedResult"
inverse-method	Class "dimRedResult"
Isomap	Isomap embedding
Isomap-class	Isomap embedding

-- K --

KamadaKawai	Graph Embedding via the Kamada Kawai Algorithm
KamadaKawai-class	Graph Embedding via the Kamada Kawai Algorithm
kPCA	Kernel PCA
kPCA-class	Kernel PCA

-- L --

LaplacianEigenmaps	Laplacian Eigenmaps
LaplacianEigenmaps-class	Laplacian Eigenmaps
LCMC	Method LCMC
LCMC-method	Method LCMC
loadDataSet	Example Data Sets for dimensionality reduction

-- M --

makeKNNgraph	makeKNNgraph
maximize_correlation	Maximize Correlation with the Axes
maximize_correlation-method	Maximize Correlation with the Axes
MDS	Metric Dimensional Scaling
MDS-class	Metric Dimensional Scaling
mean_R_NX	Method mean_R_NX
mean_R_NX-method	Method mean_R_NX
mixColor1Ramps	Mixing color ramps
mixColor2Ramps	Mixing color ramps
mixColor3Ramps	Mixing color ramps
mixColorRamps	Mixing color ramps

-- N --

ndims	Method ndims
ndims-method	Class "dimRedData"
ndims-method	Class "dimRedResult"
nMDS	Non-Metric Dimensional Scaling
nMDS-class	Non-Metric Dimensional Scaling
NNMF	Non-Negative Matrix Factorization
NNMF-class	Non-Negative Matrix Factorization
nrow-method	Class "dimRedData"

-- P --

PCA	Principal Component Analysis
PCA-class	Principal Component Analysis
PCA_L1	Principal Component Analysis with L1 error.
PCA_L1-class	Principal Component Analysis with L1 error.
plot	Plotting of dimRed* objects
plot-method	Plotting of dimRed* objects
plot.dimRed	Plotting of dimRed* objects
plot.dimRedData	Plotting of dimRed* objects
plot.dimRedResult	Plotting of dimRed* objects
plot_R_NX	plot_R_NX
predict-method	Class "dimRedResult"
print	Method print
print-method	Class "dimRedResult"

-- Q --

quality	Quality Criteria for dimensionality reduction.
quality-method	Quality Criteria for dimensionality reduction.
quality.dimRedResult	Quality Criteria for dimensionality reduction.
Q_global	Method Q_global
Q_global-method	Method Q_global
Q_local	Method Q_local
Q_local-method	Method Q_local
Q_NX	Method Q_NX
Q_NX-method	Method Q_NX

-- R --

reconstruction_error	Method reconstruction_error
reconstruction_error-method	Method reconstruction_error
reconstruction_rmse	Method reconstruction_rmse
reconstruction_rmse-method	Method reconstruction_rmse
R_NX	Method R_NX
R_NX-method	Method R_NX

-- T --

total_correlation	Method total_correlation
total_correlation-method	Method total_correlation
tSNE	t-Distributed Stochastic Neighborhood Embedding
tSNE-class	t-Distributed Stochastic Neighborhood Embedding

-- U --

UMAP	Umap embedding
UMAP-class	Umap embedding

-- misc --

[-method

Class "dimRedData"