nnet
From nnet v7.312
by Brian Ripley
Fit Neural Networks
Fit singlehiddenlayer neural network, possibly with skiplayer connections.
 Keywords
 neural
Usage
nnet(x, ...)
"nnet"(formula, data, weights, ..., subset, na.action, contrasts = NULL)
"nnet"(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 = 1.0e4, reltol = 1.0e8, ...)
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 skiplayer 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
NA
s 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 leastsquares.
 softmax

switch for softmax (loglinear model) and maximum conditional
likelihood fitting.
linout
,entropy
,softmax
andcensored
are mutually exclusive.  censored

A variant on
softmax
, in which nonzero targets mean possible classes. Thus forsoftmax
a row of(0, 1, 1)
means one example each of classes 2 and 3, but forcensored
it means one example whose class is only known to be 2 or 3.  skip
 switch to add skiplayer 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 thatrang
* 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 timeconsuming.  abstol

Stop if the fit criterion falls below
abstol
, indicating an essentially perfect fit.  reltol

Stop if the optimizer is unable to reduce the fit criterion by a
factor of at least
1  reltol
.  ...
 arguments passed to or from other methods.
Details
If the response in formula
is a factor, an appropriate classification
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
.
Optimization is done via the BFGS method of optim
.
Value

object of class
 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.
 convergence

1
if the maximum number of iterations was reached, otherwise0
.
"nnet"
or "nnet.formula"
.
Mostly internal structure, but has componentsReferences
Ripley, B. D. (1996) Pattern Recognition and Neural Networks. Cambridge.
Venables, W. N. and Ripley, B. D. (2002) Modern Applied Statistics with S. Fourth edition. Springer.
See Also
Examples
library(nnet)
# 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 = 5e4, 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 = factor(c(rep("s",50), rep("c", 50), rep("v", 50))))
ir.nn2 < nnet(species ~ ., data = ird, subset = samp, size = 2, rang = 0.1,
decay = 5e4, maxit = 200)
table(ird$species[samp], predict(ir.nn2, ird[samp,], type = "class"))
Community examples
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