| Title: | Simultaneous Model-Based Clustering and Imputation via a Progressive Expectation-Maximization Algorithm |
|---|---|
| Description: | Contains the function CUUimpute() which performs model-based clustering and imputation simultaneously. |
| Authors: | Brian C. Franczak, Ryan P. Browne and Paul D. McNicholas |
| Maintainer: | Brian C. Franczak <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.1 |
| Built: | 2024-11-28 06:28:02 UTC |
| Source: | CRAN |
Simultaneously performs model-based clustering and imputation using a Parsimonious Gaussian Mixture Model (PGMM) with CUU covariance structure.
CUUimpute(x, G = 1:3, q = 1:2, epsilon = 0.01, max.iter = 10000, known = NULL, print = TRUE)CUUimpute(x, G = 1:3, q = 1:2, epsilon = 0.01, max.iter = 10000, known = NULL, print = TRUE)
x |
A numeric matrix. |
G |
A number or vector indicating the number components to fit. |
q |
A number or vector indicating the number of latent factors to fit. |
epsilon |
The tolerance value for Aitken's acceleration. |
max.iter |
The maximum number of iterations for the PEM algorithm. A warning message is displayed if the maximum is met. |
known |
Optional. A vector of group memberships that must be numeric and whose length must be equal to the number of rows in x. (See Example I below) |
print |
Logical indicating whether or not the iteration number and the corresponding log-likelihood value should be printed. |
The PGMM with CUU covariance structure, herein referred to as the CUU model, was developed in McNicholas and Murphy (2008) for model-based clustering. The CUU model, like the other PGMMs, arises by assuming a latent Gaussian model structure for each population. As a result, the number of free parameters in CUU model's covariance structure increases linearly as the dimension of the data increases.
Browne et al. (2013) developed a Progressive Expectation-Maximization (PEM) algorithm to fit the CUU model to data with missing values. Under this parameter estimation scheme the CUU model is able to simultaneously impute and cluster a given data matrix. The CUUimpute() function fits the CUU model for a varying number of components, G, and latent factors, q, to a data matrix x. The function will run if only a data matrix is supplied however, the user is able to choose how many components and latent factors to fit, specify the tolerance limit for Aitken's acceleration, the maximum number of PEM iterations the algorithm will perform and give a vector representing the group memberships of each observation, if that information exists.
allbic |
An array containing the Bayesian Information Criterion (BIC) values for each CUU model fitted to the data. |
bic |
The BIC of the best fitting CUU model. |
G |
The number of components in the best fitting CUU model. |
q |
The number of latent factors in the best fitting CUU model. |
loglik |
A vector whose length is equal to the number of PEM iterations performed and whose elements contain the log-likelihood value on each iteration. |
gpar |
A list of the model parameters corresponding to the best fitting CUU model. |
yhat |
A data matrix with imputed values. |
u |
A matrix containing the values of the latent variables. |
zig |
A matrix giving the probabilities of group membership for each observation. Note: these probabilties are based off the model parameters of the best fitting CUU model |
map |
A vector whose length is equal to the number of observations and whose elements correspond to the group membership of each observation. |
class.table |
A cross tabulation between the predicted and true group memberships. |
iclresult |
A list containing all of the information listed above for the best fitting CUU model chosen by the Integrated Complete Likelihood (ICL) measure. Note: allbic and bic are replaced by allicl and icl. |
Brian C. Franczak, Ryan P. Browne and Paul D. McNicholas
Maintainer: Brian C. Franczak <[email protected]>
P.D. McNicholas and T.B. Murphy (2008). Parsimonious Gaussian Mixture Models. Statistics and Computing (18), 285-296.
Browne, R.P., P.D. McNicholas, and C.J. Findlay (2013). A partial EM algorithm for clustering white breads. arXiv preprint arXiv:1302.6625.
### Example I data(iiris) # loads the modified Iris data head(iiris) # displays the first six rows of the modified Iris data data(iris) # loads the original Iris data # create a vectors whose elements contain the group memberships of each flower iris.known <- as.integer(iris[,ncol(iris)]) # fit a three component CUU models to the modified Iris data output <- CUUimpute(x=iiris,G=3,q=1,print=FALSE,known=iris.known) output summary(output) # Summarizes the results names(output) # Shows what results are available output$allbic # Gives every BIC value output$bic # Gives BIC for best fitting model output$G # Gives the number of components for the best fitting CUU model output$loglik # Gives a vector whose elements are the log-likelihood at each iteration output$gpar # Gives the model parameters for the best fitting CUU model head(output$yhat) # Displays the first 6 rows of the imputed matrix output$yhat # Gives the entire imputed matrix output$class.table # Gives a classification table between the predicted and true group memberships### Example I data(iiris) # loads the modified Iris data head(iiris) # displays the first six rows of the modified Iris data data(iris) # loads the original Iris data # create a vectors whose elements contain the group memberships of each flower iris.known <- as.integer(iris[,ncol(iris)]) # fit a three component CUU models to the modified Iris data output <- CUUimpute(x=iiris,G=3,q=1,print=FALSE,known=iris.known) output summary(output) # Summarizes the results names(output) # Shows what results are available output$allbic # Gives every BIC value output$bic # Gives BIC for best fitting model output$G # Gives the number of components for the best fitting CUU model output$loglik # Gives a vector whose elements are the log-likelihood at each iteration output$gpar # Gives the model parameters for the best fitting CUU model head(output$yhat) # Displays the first 6 rows of the imputed matrix output$yhat # Gives the entire imputed matrix output$class.table # Gives a classification table between the predicted and true group memberships
Contains the function CUUimpute() which performs model-based clustering and imputation simultaneously.
| Package: | sensory |
| Type: | Package |
| Version: | 1.0 |
| Date: | 2014-08-07 |
| License: | GPL (>=2) |
This package contains two data sets collected at Compusense Inc. in Guelph, Ontario, Canada, a modified version of Fisher's Irises, and the function CUUImpute().
Brian C. Franczak, Ryan P. Browne and Paul D. McNicholas
Maintainer: Brian C. Franczak <[email protected]>
P.D. McNicholas and T.B. Murphy (2008). Parsimonious Gaussian Mixture Models. Statistics and Computing (18), 285-296.
Browne, R.P., P.D. McNicholas, and C.J. Findlay (2013). A partial EM algorithm for clustering white breads. arXiv preprint arXiv:1302.6625.
Details, examples, and references are given under CUUimpute
The brown bread data set is composed of 570 panelists and 16 products, labelled A,...,P to protect the identity of the manufacturer. Each panelist rated a subset of 6 products using the 9-point Hedonic Scale.
data(bbread)data(bbread)
data(bbread) # Loads the brown bread data set head(bbread) # Displays the first six rows of the brown bread data setdata(bbread) # Loads the brown bread data set head(bbread) # Displays the first six rows of the brown bread data set
Fisher's Irises with one measurement removed per observation. For details load data(iris,package="gclus").
data(iiris)data(iiris)
data(iiris) # Loads the modified Iris data. head(iiris) # Displays the first six rows of the modified Iris Datadata(iiris) # Loads the modified Iris data. head(iiris) # Displays the first six rows of the modified Iris Data
The white bread data is a liking study composed of 420 panelists and 12 products, labelled A,...,L to protect the identity of the manufacturer. Each panelist rated 6 white breads using the 9-point Hedonic scale.
data(wbread)data(wbread)
Browne, R.P., P.D. McNicholas, and C.J. Findlay (2013). A partial EM algorithm for clustering white breads. arXiv prerpeint arXiv:1302.6625.
data(wbread) # Loads the white bread data head(wbread) # Displays the first six rows of the white bread datadata(wbread) # Loads the white bread data head(wbread) # Displays the first six rows of the white bread data