mdatools (version 0.9.1)

simca: SIMCA one-class classification

Description

simca is used to make SIMCA (Soft Independent Modelling of Class Analogies) model for one-class classification.

Usage

simca(x, classname, ncomp = 15, center = T, scale = F, cv = NULL,
  exclcols = NULL, exclrows = NULL, x.test = NULL, c.test = NULL,
  method = "svd", rand = NULL, lim.type = "jm", alpha = 0.05,
  gamma = 0.01, info = "")

Arguments

x

a numerical matrix with data values.

classname

short text (up to 20 symbols) with class name.

ncomp

maximum number of components to calculate.

center

logical, do mean centering of data or not.

scale

logical, do sdandardization of data or not.

cv

number of segments for random cross-validation (1 for full cross-validation).

exclcols

columns to be excluded from calculations (numbers, names or vector with logical values)

exclrows

rows to be excluded from calculations (numbers, names or vector with logical values)

x.test

a numerical matrix with test data.

c.test

a vector with classes of test data objects (can be text with names of classes or logical).

method

method to compute principal components.

rand

vector with parameters for randomized PCA methods (if NULL, conventional PCA is used instead)

lim.type

which method to use for calculation of critical limits for residuals (see details)

alpha

significance level for calculating critical limits for T2 and Q residuals.

gamma

significance level for calculating outlier limits for T2 and Q residuals.

info

text with information about the model.

Value

Returns an object of simca class with following fields:

classname

a short text with class name.

modpower

a matrix with modelling power of variables.

calres

an object of class simcares with classification results for a calibration data.

testres

an object of class simcares with classification results for a test data, if it was provided.

cvres

an object of class simcares with classification results for cross-validation, if this option was chosen.

Fields, inherited from pca class:

ncomp

number of components included to the model.

ncomp.selected

selected (optimal) number of components.

loadings

matrix with loading values (nvar x ncomp).

eigenvals

vector with eigenvalues for all existent components.

expvar

vector with explained variance for each component (in percent).

cumexpvar

vector with cumulative explained variance for each component (in percent).

T2lim

statistical limit for T2 distance.

Qlim

statistical limit for Q residuals.

info

information about the model, provided by user when build the model.

Details

SIMCA is in fact PCA model with additional functionality, so simca class inherits most of the functionality of pca class. It uses critical limits calculated for Q and T2 residuals calculated for PCA model for making classification decistion.

References

S. Wold, M. Sjostrom. "SIMCA: A method for analyzing chemical data in terms of similarity and analogy" in B.R. Kowalski (ed.), Chemometrics Theory and Application, American Chemical Society Symposium Series 52, Wash., D.C., American Chemical Society, p. 243-282.

See Also

Methods for simca objects:

print.simca	shows information about the object.
summary.simca	shows summary statistics for the model.
plot.simca	makes an overview of SIMCA model with four plots.
predict.simca	applies SIMCA model to a new data.
plotModellingPower.simca	shows plot with modelling power of variables.

Methods, inherited from classmodel class:

plotPredictions.classmodel	shows plot with predicted values.
plotSensitivity.classmodel	shows sensitivity plot.
plotSpecificity.classmodel	shows specificity plot.
plotMisclassified.classmodel	shows misclassified ratio plot.

Methods, inherited from pca class:

selectCompNum.pca	set number of optimal components in the model
plotScores.pca	shows scores plot.
plotLoadings.pca	shows loadings plot.
plotVariance.pca	shows explained variance plot.
plotCumVariance.pca	shows cumulative explained variance plot.
plotResiduals.pca	shows Q vs. T2 residuals plot.

Examples

# NOT RUN {
## make a SIMCA model for Iris setosa class with full cross-validation
library(mdatools)

data = iris[, 1:4]
class = iris[, 5]

# take first 20 objects of setosa as calibration set 
se = data[1:20, ]

# make SIMCA model and apply to test set
model = simca(se, 'setosa', cv = 1)
model = selectCompNum(model, 1)

# show infromation, summary and plot overview
print(model)
summary(model)
plot(model)

# show predictions 
par(mfrow = c(2, 1))
plotPredictions(model, show.labels = TRUE)
plotPredictions(model, res = 'calres', ncomp = 2, show.labels = TRUE)
par(mfrow = c(1, 1))

# show performance, modelling power and residuals for ncomp = 2
par(mfrow = c(2, 2))
plotSensitivity(model)
plotMisclassified(model)
plotModellingPower(model, ncomp = 2, show.labels = TRUE)
plotResiduals(model, ncomp = 2)
par(mfrow = c(1, 1))

# }