cpm.all: Wrapper for Calculating Classification Performance Measures

In cpfa: Classification with Parallel Factor Analysis

Wrapper for Calculating Classification Performance Measures

Description

Applies function cpm to multiple sets of class labels. Each set of class labels is evaluated against the same set of predicted labels. Works with output from function predict.tunecpfa and calculates classification performance measures for multiple classifiers or numbers of components.

Usage

cpm.all(x, y, ...)

Arguments

x	A data frame where each column contains a set of class labels of class numeric, factor, or integer. If a set is of class factor, that set is converted to class integer in the order of factor levels with integers beginning at 0 (i.e., for binary classification, factor levels become 0 and 1; for multiclass, levels become 0, 1, 2, etc.).
y	Class labels of class numeric.
...	Additional arguments passed to function cpm for calculating classification performance measures.

Details

Wrapper function that applies function cpm to multiple sets of class labels and one other set of labels. See help file for function cpm for additional details.

Value

Returns a list with the following two elements:

cm.list	A list of confusion matrices, denoted cm, where each confusion matrix is associated with one comparison.
cpms	A data frame containing classification performance measures where each row contains measures for one comparison.

Author(s)

Matthew Asisgress <[e-mail]>

References

Sokolova, M. and Lapalme, G. (2009). A systematic analysis of performance measures for classification tasks. Information Processing and Management, 45(4), 427-437.

Examples

########## Parafac example with 3-way array and binary response ##########
## Not run: 
# set seed and simulate a three-way array related to a binary response
set.seed(5)

# define list of arguments specifying distributions for A and G weights
techlist <- list(distA = list(dname = "poisson", 
                              lambda = 3),                 # for A weights
                 distG = list(dname = "gamma", shape = 2, 
                              scale = 4))                  # for G weights

# define target correlation matrix for columns of C mode weights matrix
cormat <- matrix(c(1, .6, .6, .6, 1, .6, .6, .6, 1), nrow = 3, ncol = 3)

# simulate a three-way array connected to a response
data <- simcpfa(arraydim = c(11, 12, 100), model = "parafac", nfac = 3, 
                nclass = 2, nreps = 1e2, onreps = 10, corresp = rep(.6, 3), 
                meanpred = rep(2, 3), modes = 3, corrpred = cormat,
                technical = techlist, smethod = "eigende")

# initialize
alpha <- seq(0, 1, length = 2)
gamma <- c(0, 0.01)
cost <- c(1, 2)
method <- c("PLR", "SVM")
family <- "binomial"
parameters <- list(alpha = alpha, gamma = gamma, cost = cost)
model <- "parafac"
nfolds <- 3
nstart <- 3

# constrain first mode weights to be orthogonal
const <- c("orthog", "uncons", "uncons")

# fit Parafac models and use third mode to tune classification methods
tune.object <- tunecpfa(x = data$X[, , 1:80], y = data$y[1:80], 
                        model = model, nfac = 3, nfolds = nfolds, 
                        method = method, family = family, 
                        parameters = parameters, parallel = FALSE, 
                        const = const, nstart = nstart)
                    
# predict class labels
predict.labels <- predict(object = tune.object, newdata = data$X[, , 81:100], 
                          type = "response")
                        
# calculate performance measures for predicted class labels
yproc <- as.numeric(data$y[81:100]) - 1
evalmeasure <- cpm.all(x = predict.labels, y = yproc)

# print performance measures
evalmeasure

## End(Not run)

cpfa documentation built on March 30, 2026, 1:06 a.m.