Fit Neural Networks

Usage

nnet.formula(formula, data=NULL, ...,
             subset, na.action=na.fail, contrasts=NULL)
nnet.default(x, y, weights, size, Wts, mask,
             linout=FALSE, entropy=FALSE, softmax=FALSE, censored=FALSE,
             skip=FALSE, rang=0.7, decay=0, maxit=100,
             Hess=FALSE, trace=TRUE, MaxNWts=1000, abstol=1.0e-4,
             reltol=1.0e-4)

Arguments

formula A formula of the form class ~ x1 + x2 + ...{}
x matrix or data frame of x values for examples.
y matrix or data frame of target values for examples.
weights (case) weights for each example – if missing defaults to 1.
size number of units in the hidden layer. Can be zero if there are skip-layer units.
data Data frame from which variables specified in formula are preferentially to be taken.
subset An index vector specifying the cases to be used in the training sample. (NOTE: If given, this argument must be named.)
na.action A function to specify the action to be taken if NAs are found. The default action is for the procedure to fail. An alternative is na.omit, which leads to rejection of cases with missing values on any required variable. (NOTE: If given, this argument must be named.)
contrasts a list of contrasts to be used for some or all of the factors appearing as variables in the model formula.
Wts initial parameter vector. If missing chosen at random.
mask logical vector indicating which parameters should be optimized (default all).
linout switch for linear output units. Default logistic output units.
entropy switch for entropy (= maximum conditional likelihood) fitting. Default by least-squares.
softmax switch for softmax (log-linear model) and maximum conditional likelihood fitting. linout, entropy, softmax and censored are mutually exclusive.
censored A variant on softmax, in which non-zero targets mean possible classes. Thus for softmax a row of (0, 1, 1) means one example each of classes 2 and 3, but for censored it means one example whose class is only known to be 2 or 3.
skip switch to add skip-layer connections from input to output.
rang Initial random weights on [-rang, rang]. Value about 0.5 unless the inputs are large, in which case it should be chosen so that rang * max(|x|) is about 1.
decay parameter for weight decay. Default 0.
maxit maximum number of iterations. Default 100.
Hess If true, the Hessian of the measure of fit at the best set of weights found is returned as component Hessian.
trace switch for tracing optimization. Default TRUE.
MaxNWts The maximum allowable number of weights. There is no intrinsic limit in the code, but increasing MaxNWts will probably allow fits that are very slow and time-consuming (and perhaps uninterruptable under Windows).
abstol Stop if the fit criterion falls below abstol, indicating an esentially perfect fit.
reltol Stop if the optimizer is unable to reduce the fit criterion by a factor of at least 1 - reltol.

Description

Fit single-hidden-layer neural network, possibly with skip-layer connections.

Details

If the response in formula is a factor, an appropriate classfication network is constructed; this has one output and entropy fit if the number of levels is two, and a number of outputs equal to the number of classes and a softmax output stage for more levels. If the response is not a factor, it is passed on unchanged to nnet.default.

A quasi-Newton optimizer is used, written in C.

Value

object of class nnet or nnet.formula. Mostly internal structure, but has components

wts the best set of weights found
value value of fitting criterion plus weight decay term.
fitted.values the fitted values for the training data.
residuals the residuals for the training data.

See Also

predict.nnet, nnet.Hess

Examples

data(iris3)
# use half the iris data
ir <- rbind(iris3[,,1],iris3[,,2],iris3[,,3])
targets <- class.ind( c(rep("s", 50), rep("c", 50), rep("v", 50)) )
samp <- c(sample(1:50,25), sample(51:100,25), sample(101:150,25))
ir1 <- nnet(ir[samp,], targets[samp,], size=2, rang=0.1, 
            decay=5e-4, maxit=200)
test.cl <- function(true, pred){
        true <- max.col(true)
        cres <- max.col(pred)
        table(true, cres)
}
test.cl(targets[-samp,], predict(ir1, ir[-samp,]))

# or
ird <- data.frame(rbind(iris3[,,1], iris3[,,2], iris3[,,3]),
	species=c(rep("s",50), rep("c", 50), rep("v", 50)))
ir.nn2 <- nnet(species ~ ., data=ird, subset=samp, size=2, rang=0.1, 
            decay=5e-4, maxit=200)
table(ird$species[-samp], predict(ir.nn2, ird[-samp,], type="class"))

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