\HeaderA{nls}{Nonlinear Least Squares}{nls}
\keyword{nonlinear}{nls}
\keyword{regression}{nls}
\keyword{models}{nls}
\begin{Description}\relax
Determine the nonlinear least-squares estimates of the nonlinear model
parameters and return a class \code{nls} object.
\end{Description}
\begin{Usage}
\begin{verbatim}
nls(formula, data, start, control, algorithm,
    trace, subset, weights, na.action, model,
    lower, upper, ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{formula}] a nonlinear model formula including variables and parameters
\item[\code{data}] an optional data frame in which to evaluate the variables in
\code{formula}
\item[\code{start}] a named list or named numeric vector of starting estimates
\item[\code{control}] an optional list of control settings.  See
\code{nls.control} for the names of the settable control values and
their effect.
\item[\code{algorithm}] character string specifying the algorithm to use.
The default algorithm is a Gauss-Newton algorithm. Other possible
values are \code{"plinear"} for the Golub-Pereyra algorithm for
partially linear least-squares models and \code{"port"} for the
"nl2sol" algorithm from the Port package.
\item[\code{trace}] logical value indicating if a trace of the iteration
progress should be printed.  Default is \code{FALSE}.  If
\code{TRUE} the residual sum-of-squares and the parameter values
are printed at the conclusion of each iteration.  When the
\code{"plinear"} algorithm is used, the conditional estimates of
the linear parameters are printed after the nonlinear
parameters.  When the \code{"port"} algorithms are used the
objective function value printed is half the residual sum-of-squares.
\item[\code{subset}] an optional vector specifying a subset of observations
to be used in the fitting process.
\item[\code{weights}] an optional numeric vector of (fixed) weights.  When
present, the objective function is weighted least squares. \emph{not
yet implemented}
\item[\code{na.action}] a function which indicates what should happen
when the data contain \code{NA}s.  The default is set by
the \code{na.action} setting of \code{\LinkA{options}{options}}, and is
\code{\LinkA{na.fail}{na.fail}} if that is unset.  The \dQuote{factory-fresh}
default is \code{\LinkA{na.omit}{na.omit}}.  Value \code{\LinkA{na.exclude}{na.exclude}}
can be useful.
\item[\code{model}] logical.  If true, the model frame is returned as part of
the object. Default is \code{FALSE}
\item[\code{lower, upper}] vector of lower and upper bounds, replicated to be as long as
\code{start}.  If unspecified, all parameters are assumed to be
unconstrained.  Bounds can only be used with the \code{"port"}
algorithm.  They are ignored, with a warning, if given for other
algorithms.
\item[\code{...}] Additional optional arguments.  None are used at present.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
\bold{Do not use \code{nls} on artificial "zero-residual" data.}

The \code{nls} function uses a relative-offset convergence criterion
that compares the numerical imprecision at the current parameter
estimates to the residual sum-of-squares.  This performs well on data of
the form \deqn{y=f(x,\theta)+\epsilon}{y = f(x, theta) + eps} (with
\code{var(eps) > 0}).  It
fails to indicate convergence on data of the form
\deqn{y=f(x,\theta)}{y = f(x, theta)} because the criterion amounts to
comparing two components of the round-off error.  If you wish to test
\code{nls} on artificial data please add a noise component, as shown
in the example below.

An \code{nls} object is a type of fitted model object.  It has methods
for the generic functions \code{\LinkA{coef}{coef}}, \code{\LinkA{formula}{formula}},
\code{\LinkA{resid}{resid}}, \code{\LinkA{print}{print}}, \code{\LinkA{summary}{summary}},
\code{\LinkA{AIC}{AIC}}, \code{\LinkA{fitted}{fitted}} and \code{\LinkA{vcov}{vcov}}.

Variables in \code{formula} are looked for first in \code{data}, then
the environment of \code{formula} (added in 1.9.1) and finally along
the search path.  Functions in \code{formula} are searched for first
in the environment of \code{formula} (added in 1.9.1) and then along
the search path.
\end{Details}
\begin{Value}
A list of
\begin{ldescription}
\item[\code{m}] an \code{nlsModel} object incorporating the model
\item[\code{data}] the expression that was passed to \code{nls} as the data
argument.  The actual data values are present in the environment of
the \code{m} component.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Douglas M. Bates and Saikat DebRoy
\end{Author}
\begin{References}\relax
Bates, D.M. and Watts, D.G. (1988)
\emph{Nonlinear Regression Analysis and Its Applications},
Wiley

Bates, D. M. and Chambers, J. M. (1992)
\emph{Nonlinear models.}
Chapter 10 of \emph{Statistical Models in S}
eds J. M. Chambers and T. J. Hastie, Wadsworth \& Brooks/Cole.

\url{http://netlib.bell-labs.com/netlib/port/} for the Port library
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{nlsModel}{nlsModel}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
DNase1 <- subset(DNase, Run == 1)
## using a selfStart model
fm1DNase1 <- nls( density ~ SSlogis(log(conc), Asym, xmid, scal), DNase1)
summary( fm1DNase1 )
## using conditional linearity
fm2DNase1 <- nls( density ~ 1/(1 + exp((xmid - log(conc))/scal)),
                  data = DNase1,
                  start = list(xmid = 0, scal = 1),
                  alg = "plinear", trace = TRUE)
summary( fm2DNase1 )
## without conditional linearity
fm3DNase1 <- nls( density ~ Asym/(1 + exp((xmid - log(conc))/scal)),
                  data = DNase1,
                  start = list(Asym = 3, xmid = 0, scal = 1),
                  trace = TRUE)
summary( fm3DNase1 )
## using the nl2sol algorithm
fm4DNase1 <- nls( density ~ Asym/(1 + exp((xmid - log(conc))/scal)),
                  data = DNase1,
                  start = list(Asym = 3, xmid = 0, scal = 1),
                  trace = TRUE, algorithm = "port")
summary(fm4DNase1)

## weighted nonlinear regression
Treated <- Puromycin[Puromycin$state == "treated", ]
weighted.MM <- function(resp, conc, Vm, K)
{
    ## Purpose: exactly as white book p.451 -- RHS for nls()
    ##  Weighted version of Michaelis-Menten model
    ## ------------------------------------------------------------
    ## Arguments: 'y', 'x' and the two parameters (see book)
    ## ------------------------------------------------------------
    ## Author: Martin Maechler, Date: 23 Mar 2001, 18:48

    pred <- (Vm * conc)/(K + conc)
    (resp - pred) / sqrt(pred)
}

Pur.wt <- nls( ~ weighted.MM(rate, conc, Vm, K), data = Treated,
              start = list(Vm = 200, K = 0.1),
              trace = TRUE)

## The two examples below show that you can fit a model to
## artificial data with noise but not to artificial data
## without noise.
x = 1:10
y = x                                  # perfect fit
yeps = y + rnorm(length(y), sd = 0.01) # added noise
nls(yeps ~ a + b*x, start = list(a = 0.12345, b = 0.54321),
     trace = TRUE)
## Not run: 
nls(y ~ a + b*x, start = list(a = 0.12345, b = 0.54321),
     trace = TRUE)
## End(Not run)       
\end{ExampleCode}
\end{Examples}

