A better ‘nls’ (?)

July 5, 2012
By

(This article was first published on Rmazing, and kindly contributed to R-bloggers)

Those that do a lot of nonlinear regression will love the nls function of R. In most of the cases it works really well, but there are some mishaps that can occur when using bad starting values for the parameters. One of the most dreaded is the “singular gradient matrix at initial parameter estimates” which brings the function to a stop because the gradient check in stats:::nlsModel will terminate if the QR decomposition is not of full column rank.

Nearly all nonlinear fitting programs out there use the Levenberg-Marquardt algorithm for nonlinear regression. This is because its switching between Gauss-Newton and gradient descent is highly robust against far-off-optimal starting values.  Unfortunately, the standard nls function has no LM implemented, instead it houses the Gauss-Newton type, the PORT routines and a partial linear fitter. The fabulous minpack.lm package from Katherine M. Mullen offers an R frontend to a Fortran LM implementation of the MINPACK package. The nls.lm function must be supplied with an objective function that returns a vector of residuals to be minimized. Together with Kate I developed a function nlsLM that has the gee wizz formulaic interface of nls, but it calls LM instead of Gauss-Newton. This has some advantages as we will see below.  The function returns the usual result of class ‘nls’, and due to some modifications, all standard generics work. The modifications were made so that the formula is transformed into a function that returns a vector of (weighted) residuals whose sum square is minimized by nls.lm. The optimized parameters are then transferred to stats:::nlsModel in order to obtain an object of class ‘nlsModel’. The internal C  functions C_nls_iter and stats:::nls_port_fit were removed to avoid subsequent “Gauss-Newton”, “port” or “plinear” optimization of nlsModel.

So, what’s similar and what’s, well, better…

library(minpack.lm)
### Examples from 'nls' doc ###
DNase1 <- subset(DNase, Run == 1)
fm1DNase1 <- nlsLM(density ~ Asym/(1 + exp((xmid - log(conc))/scal)), 
data = DNase1, start = list(Asym = 3, xmid = 0, scal = 1))
## all generics are applicable
coef(fm1DNase1)
confint(fm1DNase1)
deviance(fm1DNase1)
df.residual(fm1DNase1)
fitted(fm1DNase1)
formula(fm1DNase1)
logLik(fm1DNase1)
predict(fm1DNase1)
print(fm1DNase1)
profile(fm1DNase1)
residuals(fm1DNase1)
summary(fm1DNase1)
update(fm1DNase1)
vcov(fm1DNase1)
weights(fm1DNase1)

nlsLM can fit zero noise data, when nls fails:

x <- 1:10
y <- 2*x + 3                           
nls(y ~ a + b * x, start = list(a = 0.12345, b = 0.54321))
nlsLM(y ~ a + b * x, start = list(a = 0.12345, b = 0.54321))

Nonlinear regression model
model: y ~ a + b * x
data: parent.frame()
a b
3 2
residual sum-of-squares: 0

Number of iterations to convergence: 3
Achieved convergence tolerance: 1.49e-08

nlsLM often converges when nls gives the dreaded "singular gradient" error.
Example taken from here:

x <- 0:140
y <- 200 / (1 + exp(17 - x)/2) * exp(-0.02*x)
yeps <- y + rnorm(length(y), sd = 2)
nls(yeps ~ p1 / (1 + exp(p2 - x)) * exp(p4 * x), start=list(p1=410,p2=18,p4=-.03))

Optimal starting parameters work:
Nonlinear regression model
model: yeps ~ p1/(1 + exp(p2 - x)) * exp(p4 * x)
data: parent.frame()
p1 p2 p4
200.67285 16.32430 -0.02005
residual sum-of-squares: 569

Number of iterations to convergence: 6
Achieved convergence tolerance: 2.611e-07

But off-optimal parameters give error:

nls(yeps ~ p1 / (1 + exp(p2 - x)) * exp(p4 * x), start=list(p1=10,p2=18,p4=-.03))

Fehler in nls(yeps ~ p1/(1 + exp(p2 - x)) * exp(p4 * x), start = list(p1 = 10, :
singulärer Gradient

nlsLM is more robust with these starting parameters:

nlsLM(yeps ~ p1 / (1 + exp(p2 - x)) * exp(p4 * x), start=list(p1=10,p2=18,p4=-.03))

Nonlinear regression model
model: yeps ~ p1/(1 + exp(p2 - x)) * exp(p4 * x)
data: parent.frame()
p1 p2 p4
200.67285 16.32430 -0.02005
residual sum-of-squares: 569

Number of iterations to convergence: 10
Achieved convergence tolerance: 1.49e-08

Have fun!
Cheers, Andrej

 

 


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