{gslnls}: GSL Multi-Start Nonlinear Least-Squares Fitting in R

The {gslnls}-package provides R bindings to nonlinear least-squares optimization with the GNU Scientific Library (GSL). The function gsl_nls() solves small to moderate sized nonlinear least-squares problems with the gsl_multifit_nlinear interface with built-in support for multi-start optimization. For large problems, where factoring the full Jacobian matrix becomes prohibitively expensive, the gsl_nls_large() function can be used to solve the system with the gsl_multilarge_nlinear interface. The gsl_nls_large() function is also appropriate for systems with sparse structure in the Jacobian matrix.

The following trust region methods to solve nonlinear least-squares problems are available in gsl_nls() (and gsl_nls_large()):

Levenberg-Marquardt
Levenberg-Marquardt with geodesic acceleration
Dogleg
Double dogleg
Two Dimensional Subspace
Steihaug-Toint Conjugate Gradient (only available in gsl_nls_large())

The Tunable parameters available for the trust method algorithms can be modified from R in order to help accelerating convergence for a specific problem at hand.

See the Nonlinear Least-Squares Fitting chapter in the GSL reference manual for a comprehensive overview of the gsl_multifit_nlinear and gsl_multilarge_nlinear interfaces and the relevant mathematical background.

Installation from source

System requirements

When installing the R-package from source, verify that GSL (>= 2.2) is installed on the system, e.g. on Ubuntu/Debian Linux:

gsl-config --version

If GSL (>= 2.2) is not available on the system, install GSL from a pre-compiled binary package (see the examples below) or install GSL from source by downloading the latest stable release (https://www.gnu.org/software/gsl/) and following the installation instructions in the included README and INSTALL files.

GSL installation examples

Ubuntu, Debian

sudo apt-get install libgsl-dev

macOS

brew install gsl

Fedora, RedHat, CentOS

yum install gsl-devel

Windows

A binary version of GSL (2.7) can be installed using the Rtools package manager (see e.g. https://github.com/r-windows/docs/blob/master/rtools40.md):

pacman -S mingw-w64-{i686,x86_64}-gsl

On windows, the environment variable LIB_GSL must be set to the parent of the directory containing libgsl.a. Note that forward instead of backward slashes should be used in the directory path (e.g. C:/rtools43/x86_64-w64-mingw32.static.posix).

R-package installation

With GSL available, install the R-package from source with:

## Install latest CRAN release:
install.packages("gslnls", type = "source")

or install the latest development version from GitHub with:

## Install latest GitHub development version:
# install.packages("devtools")
devtools::install_github("JorisChau/gslnls")

Installation from binary

On windows and some macOS builds, the R-package can be installed from CRAN as a binary package. In this case, GSL does not need to be available on the system.

## Install latest CRAN release:
install.packages("gslnls")

Example usage

Example 1: Exponential model

Data

The code below simulates noisy observations $y_1,\ldots,y_n$ from an exponential model with additive (i.i.d.) Gaussian noise according to:

$\left\ \begin{aligned} f_i & = A \cdot \exp(-\lambda \cdot x_i) + b, & i = 1,\ldots, n \ y_i & = f_i + \epsilon_i, & \epsilon_i \overset{\text{iid}}{\sim} N(0,\sigma^2) \end{aligned} \right.$

The exponential model parameters are set to , $\lambda = 1.5$ , , with a noise standard deviation of $\sigma = 0.25$ .

set.seed(1)
n <- 25
x <- (seq_len(n) - 1) * 3 / (n - 1)
f <- function(A, lam, b, x) A * exp(-lam * x) + b
y <- f(A = 5, lam = 1.5, b = 1, x) + rnorm(n, sd = 0.25)

Model fit

The exponential model is fitted to the data using the gsl_nls() function by passing the nonlinear model as a two-sided formula and providing starting parameters for the model parameters $A, \lambda, b$ analogous to an nls() function call.

library(gslnls)

ex1_fit <- gsl_nls(
  fn = y ~ A * exp(-lam * x) + b,    ## model formula
  data = data.frame(x = x, y = y),   ## model fit data
  start = c(A = 0, lam = 0, b = 0)   ## starting values
)

ex1_fit
#> Nonlinear regression model
#>   model: y ~ A * exp(-lam * x) + b
#>    data: data.frame(x = x, y = y)
#>     A   lam     b 
#> 4.893 1.417 1.010 
#>  residual sum-of-squares: 1.316
#> 
#> Algorithm: multifit/levenberg-marquardt, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 9 
#> Achieved convergence tolerance: 0

Here, the nonlinear least squares problem has been solved with the Levenberg-Marquardt algorithm (default) in the gsl_multifit_nlinear interface using the following control parameters:

## default control parameters
gsl_nls_control() |> str()
#> List of 21
#>  $ maxiter        : int 100
#>  $ scale          : chr "more"
#>  $ solver         : chr "qr"
#>  $ fdtype         : chr "forward"
#>  $ factor_up      : num 2
#>  $ factor_down    : num 3
#>  $ avmax          : num 0.75
#>  $ h_df           : num 1.49e-08
#>  $ h_fvv          : num 0.02
#>  $ xtol           : num 1.49e-08
#>  $ ftol           : num 1.49e-08
#>  $ gtol           : num 1.49e-08
#>  $ mstart_n       : int 30
#>  $ mstart_p       : int 5
#>  $ mstart_q       : int 3
#>  $ mstart_r       : num 4
#>  $ mstart_s       : int 2
#>  $ mstart_tol     : num 0.25
#>  $ mstart_maxiter : int 10
#>  $ mstart_maxstart: int 250
#>  $ mstart_minsp   : int 1

Run ?gsl_nls_control or check the GSL reference manual for further details on the available tuning parameters to control the trust region algorithms.

Object methods

The fitted model object returned by gsl_nls() is of class "gsl_nls", which inherits from class "nls". For this reason, generic functions such as anova, coef, confint, deviance, df.residual, fitted, formula, logLik, predict, print profile, residuals, summary, vcov and weights are also applicable for models fitted with gsl_nls().

## model summary
summary(ex1_fit)
#> 
#> Formula: y ~ A * exp(-lam * x) + b
#> 
#> Parameters:
#>     Estimate Std. Error t value Pr(>|t|)    
#> A     4.8930     0.1811  27.014  < 2e-16 ***
#> lam   1.4169     0.1304  10.865 2.61e-10 ***
#> b     1.0097     0.1092   9.246 4.92e-09 ***
#> ---
#> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
#> 
#> Residual standard error: 0.2446 on 22 degrees of freedom
#> 
#> Number of iterations to convergence: 9 
#> Achieved convergence tolerance: 0

## asymptotic confidence intervals
confint(ex1_fit)
#>         2.5 %   97.5 %
#> A   4.5173851 5.268653
#> lam 1.1464128 1.687314
#> b   0.7832683 1.236216

The predict method extends the existing predict.nls method by allowing for calculation of asymptotic confidence and prediction (tolerance) intervals in addition to prediction of the expected response:

## asymptotic prediction intervals
predict(ex1_fit, interval = "prediction", level = 0.95)
#>            fit       lwr      upr
#>  [1,] 5.902761 5.2670162 6.538506
#>  [2,] 5.108572 4.5388041 5.678340
#>  [3,] 4.443289 3.8987833 4.987794
#>  [4,] 3.885988 3.3479065 4.424069
#>  [5,] 3.419142 2.8812430 3.957042
....

The new confintd method can be used to evaluate asymptotic confidence intervals of derived (or transformed) parameters based on the delta method, i.e. a first-order (Taylor) approximation of the function of the parameters:

## delta method confidence intervals
confintd(ex1_fit, expr = c("b", "A + b", "log(lam)"), level = 0.95)
#>                fit       lwr       upr
#> b        1.0097419 0.7832683 1.2362155
#> A + b    5.9027612 5.5194278 6.2860945
#> log(lam) 0.3484454 0.1575657 0.5393251

Jacobian calculation

If the jac argument in gsl_nls() is undefined, the Jacobian matrix used to solve the trust region subproblem is approximated by forward (or centered) finite differences. Instead, an analytic Jacobian can be passed to jac by defining a function that returns the $(n \times p)$ -dimensional Jacobian matrix of the nonlinear model fn, where the first argument must be the vector of parameters of length .

In the exponential model example, the Jacobian matrix is a $(50 \times 3)$ -dimensional matrix $[\boldsymbol{J}_{ij}]_{ij}$ with rows:

$\boldsymbol{J}_i \= \\left[ \frac{\partial f_i}{\partial A}, \frac{\partial f_i}{\partial \lambda}, \frac{\partial f_i}{\partial b} \right] \= \\left[ \exp(-\lambda \cdot x_i), -A \cdot \exp(-\lambda \cdot x_i) \cdot x_i, 1 \right]$

which is encoded in the following call to gsl_nls():

## analytic Jacobian (1)
gsl_nls(
  fn = y ~ A * exp(-lam * x) + b,    ## model formula
  data = data.frame(x = x, y = y),   ## model fit data
  start = c(A = 0, lam = 0, b = 0),  ## starting values
  jac = function(par, x) with(as.list(par), cbind(A = exp(-lam * x), lam = -A * x * exp(-lam * x), b = 1)),
  x = x                              ## argument passed to jac
)
#> Nonlinear regression model
#>   model: y ~ A * exp(-lam * x) + b
#>    data: data.frame(x = x, y = y)
#>     A   lam     b 
#> 4.893 1.417 1.010 
#>  residual sum-of-squares: 1.316
#> 
#> Algorithm: multifit/levenberg-marquardt, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 9 
#> Achieved convergence tolerance: 6.661e-16

If the model formula fn can be derived with stats::deriv(), then the analytic Jacobian in jac can be computed automatically using symbolic differentiation and no manual calculations are necessary. To evaluate jac by means of symbolic differentiation, set jac = TRUE:

## analytic Jacobian (2)
gsl_nls(
  fn = y ~ A * exp(-lam * x) + b,    ## model formula
  data = data.frame(x = x, y = y),   ## model fit data
  start = c(A = 0, lam = 0, b = 0),  ## starting values
  jac = TRUE                         ## symbolic derivation
)
#> Nonlinear regression model
#>   model: y ~ A * exp(-lam * x) + b
#>    data: data.frame(x = x, y = y)
#>     A   lam     b 
#> 4.893 1.417 1.010 
#>  residual sum-of-squares: 1.316
#> 
#> Algorithm: multifit/levenberg-marquardt, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 9 
#> Achieved convergence tolerance: 6.661e-16

Alternatively, a self-starting nonlinear model (see ?selfStart) can be passed to gsl_nls(). In this case, the Jacobian matrix is evaluated from the "gradient" attribute of the self-starting model object:

## self-starting model
ss_fit <- gsl_nls(
  fn =  y ~ SSasymp(x, Asym, R0, lrc),    ## model formula
  data = data.frame(x = x, y = y)         ## model fit data
)

ss_fit
#> Nonlinear regression model
#>   model: y ~ SSasymp(x, Asym, R0, lrc)
#>    data: data.frame(x = x, y = y)
#>   Asym     R0    lrc 
#> 1.0097 5.9028 0.3484 
#>  residual sum-of-squares: 1.316
#> 
#> Algorithm: multifit/levenberg-marquardt, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 1 
#> Achieved convergence tolerance: 1.068e-13

The self-starting model SSasymp() uses a different model parameterization (A = R0 - Asym, lam = exp(lrc), b = Asym), but the fitted models are equivalent. Also, when using a self-starting model, no starting values need to be provided.

Remark: confidence intervals for the coefficients in the original model parameterization can be evaluated with the confintd method:

## delta method confidence intervals
confintd(ss_fit, expr = c("R0 - Asym", "exp(lrc)", "Asym"), level = 0.95)
#>                fit       lwr      upr
#> R0 - Asym 4.893019 4.5173851 5.268653
#> exp(lrc)  1.416863 1.1464128 1.687314
#> Asym      1.009742 0.7832683 1.236216

Multi-start optimization

In addition to single-start NLS optimization, the gsl_nls() function has built-in support for multi-start optimization. For multi-start optimization, instead of a list or vector of fixed start parameters, pass a list or matrix of start parameter ranges to the argument start:

gsl_nls(
  fn = y ~ A * exp(-lam * x) + b,    ## model formula
  data = data.frame(x = x, y = y),   ## model fit data
  start = list(A = c(-100, 100), lam = c(-5, 5), b = c(-10, 10))   ## multi-start
)
#> Nonlinear regression model
#>   model: y ~ A * exp(-lam * x) + b
#>    data: data.frame(x = x, y = y)
#>     A   lam     b 
#> 4.893 1.417 1.010 
#>  residual sum-of-squares: 1.316
#> 
#> Algorithm: multifit/levenberg-marquardt, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 2 
#> Achieved convergence tolerance: 6.106e-14

The multi-start procedure is a modified version of the algorithm described in Hickernell and Yuan (1997), see ?gsl_nls for additional details. If start contains missing (or infinite) values, the multi-start algorithm is executed without fixed parameter ranges for the missing parameters. More precisely, the ranges are initialized to the unit interval and dynamically increased or decreased in each major iteration of the multi-start algorithm.

gsl_nls(
  fn = y ~ A * exp(-lam * x) + b,    ## model formula
  data = data.frame(x = x, y = y),   ## model fit data
  start = list(A = NA, lam = NA, b = NA)   ## dynamic multi-start
)
#> Nonlinear regression model
#>   model: y ~ A * exp(-lam * x) + b
#>    data: data.frame(x = x, y = y)
#>     A   lam     b 
#> 4.893 1.417 1.010 
#>  residual sum-of-squares: 1.316
#> 
#> Algorithm: multifit/levenberg-marquardt, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 3 
#> Achieved convergence tolerance: 0

Remark: the dynamic multi-start procedure is not expected to always return a global minimum of the NLS objective. Especially when the objective function contains many local optima, the multi-start algorithm may be unable to select parameter ranges that include the global minimizing solution.

Example 2: Gaussian function

Data

The following code generates noisy observations $y_1,\ldots,y_n$ from a Gaussian function with multiplicative independent Gaussian noise according to the model:

$\left\ \begin{aligned} f_i & = a \cdot \exp\left(-\frac{(x_i - b)^2}{2c^2}\right), & i = 1,\ldots, n \ y_i & = f_i \cdot \epsilon_i, & \epsilon_i \overset{\text{iid}}{\sim} N(1,\sigma^2) \end{aligned} \right.$

The parameters of the Gaussian model function are set to , , , with noise standard deviation $\sigma = 0.1$ (see also https://www.gnu.org/software/gsl/doc/html/nls.html#geodesic-acceleration-example-2).

set.seed(1)
n <- 50
x <- seq_len(n) / n
f <- function(a, b, c, x) a * exp(-(x - b)^2 / (2 * c^2))
y <- f(a = 5, b = 0.4, c = 0.15, x) * rnorm(n, mean = 1, sd = 0.1)

Model fit

Using the default Levenberg-Marquardt algorithm (without geodesic acceleration), the nonlinear Gaussian model can be fitted with a call to gsl_nls() analogous to the previous example. Here, the trace argument is activated in order to trace the sum of squared residuals (ssr) and parameter estimates (par) at each iteration of the algorithm.

## Levenberg-Marquardt (default)
ex2a_fit <- gsl_nls(
  fn = y ~ a * exp(-(x - b)^2 / (2 * c^2)), ## model formula
  data = data.frame(x = x, y = y),          ## model fit data
  start = c(a = 1, b = 0, c = 1),           ## starting values
  trace = TRUE                              ## verbose output
)
#> iter   1: ssr = 174.476, par = (2.1711, 3.31169, -4.12254)
#> iter   2: ssr = 171.29, par = (1.85555, 2.84851, -5.66642)
#> iter   3: ssr = 168.703, par = (1.93316, 2.34745, -6.33662)
#> iter   4: ssr = 167.546, par = (1.84665, 1.24131, -7.399)
#> iter   5: ssr = 166.799, par = (1.87948, 0.380488, -7.61723)
#> iter   6: ssr = 165.623, par = (1.90658, -2.00515, -7.19306)
#> iter   7: ssr = 163.944, par = (2.18675, -3.19622, -5.38804)
#> iter   8: ssr = 161.679, par = (2.41824, -3.1487, -5.03149)
#> iter   9: ssr = 159.955, par = (2.67372, -3.18703, -4.20169)
#> iter  10: ssr = 157.391, par = (3.1083, -2.84066, -3.10574)
#> iter  11: ssr = 153.131, par = (3.54614, -2.38071, -2.53824)
#> iter  12: ssr = 150.129, par = (4.02799, -1.97822, -1.96376)
#> iter  13: ssr = 146.735, par = (4.49887, -1.35879, -1.39554)
#> iter  14: ssr = 142.928, par = (3.14455, -0.573017, -1.08117)
#> iter  15: ssr = 124.562, par = (2.14743, 0.465351, -0.443335)
#> iter  16: ssr = 102.183, par = (3.74451, 0.263346, 0.353849)
#> iter  17: ssr = 35.4869, par = (3.49962, 0.437339, 0.18613)
#> iter  18: ssr = 9.24985, par = (4.41273, 0.381446, 0.16023)
#> iter  19: ssr = 3.13669, par = (4.94382, 0.40041, 0.150317)
#> iter  20: ssr = 2.7623, par = (5.11741, 0.397815, 0.14729)
#> iter  21: ssr = 2.75831, par = (5.13786, 0.397886, 0.146865)
#> iter  22: ssr = 2.7583, par = (5.1389, 0.397884, 0.146831)
#> iter  23: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> iter  24: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> iter  25: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> iter  26: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> *******************
#> summary from method 'multifit/levenberg-marquardt'
#> number of iterations: 26
#> reason for stopping: input domain error
#> initial ssr = 210.146
#> final ssr = 2.7583
#> ssr/dof = 0.0586872
#> ssr achieved tolerance = 8.88178e-16
#> function evaluations: 125
#> jacobian evaluations: 0
#> fvv evaluations: 0
#> status = success
#> *******************

ex2a_fit
#> Nonlinear regression model
#>   model: y ~ a * exp(-(x - b)^2/(2 * c^2))
#>    data: data.frame(x = x, y = y)
#>      a      b      c 
#> 5.1389 0.3979 0.1468 
#>  residual sum-of-squares: 2.758
#> 
#> Algorithm: multifit/levenberg-marquardt, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 26 
#> Achieved convergence tolerance: 8.882e-16

Geodesic acceleration

The nonlinear model can also be fitted using the Levenberg-Marquardt algorithm with geodesic acceleration by changing the default algorithm = "lm" to algorithm = "lmaccel".

## Levenberg-Marquardt w/ geodesic acceleration
ex2b_fit <- gsl_nls(
  fn = y ~ a * exp(-(x - b)^2 / (2 * c^2)), ## model formula
  data = data.frame(x = x, y = y),          ## model fit data
  start = c(a = 1, b = 0, c = 1),           ## starting values
  algorithm = "lmaccel",                    ## algorithm
  trace = TRUE                              ## verbose output
)
#> iter   1: ssr = 158.039, par = (1.58476, 0.502555, 0.511498)
#> iter   2: ssr = 126.469, par = (1.8444, 0.366374, 0.403898)
#> iter   3: ssr = 77.0115, par = (2.5025, 0.392374, 0.272717)
#> iter   4: ssr = 26.4036, par = (3.64063, 0.394564, 0.205619)
#> iter   5: ssr = 5.35492, par = (4.63506, 0.396865, 0.16366)
#> iter   6: ssr = 2.82529, par = (5.05578, 0.397909, 0.149333)
#> iter   7: ssr = 2.75877, par = (5.13246, 0.397896, 0.147057)
#> iter   8: ssr = 2.7583, par = (5.13862, 0.397885, 0.146843)
#> iter   9: ssr = 2.7583, par = (5.13893, 0.397884, 0.14683)
#> iter  10: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> iter  11: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> iter  12: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> *******************
#> summary from method 'multifit/levenberg-marquardt+accel'
#> number of iterations: 12
#> reason for stopping: input domain error
#> initial ssr = 210.146
#> final ssr = 2.7583
#> ssr/dof = 0.0586872
#> ssr achieved tolerance = 3.24185e-14
#> function evaluations: 76
#> jacobian evaluations: 0
#> fvv evaluations: 0
#> status = success
#> *******************

ex2b_fit
#> Nonlinear regression model
#>   model: y ~ a * exp(-(x - b)^2/(2 * c^2))
#>    data: data.frame(x = x, y = y)
#>      a      b      c 
#> 5.1389 0.3979 0.1468 
#>  residual sum-of-squares: 2.758
#> 
#> Algorithm: multifit/levenberg-marquardt+accel, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 12 
#> Achieved convergence tolerance: 3.242e-14

With geodesic acceleration enabled the method converges after 12 iterations, whereas the method without geodesic acceleration required 26 iterations. This indicates that the nonlinear least-squares solver benefits (substantially) from the geodesic acceleration correction.

Second directional derivative

By default, if the fvv argument is undefined, the second directional derivative used to calculate the geodesic acceleration correction is approximated by forward (or centered) finite differences. To use an analytic expression for , a function returning the -dimensional vector of second directional derivatives of the nonlinear model can be passed to fvv. The first argument of the function must be the vector of parameters of length and the second argument must be the velocity vector, also of length .

For the Gaussian model function, the matrix of second partial derivatives, i.e. the Hessian, is given by (cf. https://www.gnu.org/software/gsl/doc/html/nls.html#geodesic-acceleration-example-2):

$\boldsymbol{H}_{f_i} \= \ \left[\begin{matrix} \frac{\partial^2 f_i}{\partial a^2} & \frac{\partial^2 f_i}{\partial a \partial b} & \frac{\partial^2 f_i}{\partial a \partial c} \ & \frac{\partial^2 f_i}{\partial b^2} & \frac{\partial^2 f_i}{\partial b \partial c} \ & & \frac{\partial^2 f_i}{\partial c^2} \end{matrix}\right] \= \ \left[\begin{matrix} 0 & \frac{z_i}{c} e_i & \frac{z_i^2}{c} e_i \ & -\frac{a}{c^2} (1 - z_i^2) e_i & -\frac{a}{c^2} z_i (2 - z_i^2) e_i \ & & -\frac{a}{c^2} z_i^2 (3 - z_i^2) e_i \end{matrix}\right]$

where the lower half of the Hessian matrix is omitted since it is symmetric and where we use the notation,

$\begin{aligned} z_i & \= \\frac{x_i - b}{c} \ e_i & \= \\exp\left(-\frac{1}{2}z_i^2 \right) \end{aligned}$

Based on the Hessian matrix, the second directional derivative of , with $i = 1,\ldots,n$ , becomes:

$\begin{aligned} D_v^2 f_i & \= \\sum_{j,k} v_{\theta_j}v_{\theta_k} \frac{\partial^2 f_i}{\partial \theta_j \partial \theta_k} \ & \= \v_a^2 \frac{\partial^2 f_i}{\partial a^2} + 2 v_av_b\frac{\partial^2 f_i}{\partial a \partial b} + 2v_av_c\frac{\partial^2 f_i}{\partial a \partial c} + v_b^2\frac{\partial^2 f_i}{\partial b^2} + 2v_bv_c\frac{\partial^2 f_i}{\partial b \partial c} + v_c^2\frac{\partial^2 f_i}{\partial c^2} \ & \= \2v_a v_b\frac{z_i}{c} e_i + 2v_av_c \frac{z_i^2}{c} e_i - v_b^2\frac{a}{c^2} (1 - z_i^2) e_i - 2v_bv_c \frac{a}{c^2} z_i (2 - z_i^2) e_i - v_c^2\frac{a}{c^2} z_i^2 (3 - z_i^2) e_i \end{aligned}$

which can be encoded using gsl_nls() as follows:

## second directional derivative
fvv <- function(par, v, x) {
  with(as.list(par), {
    zi <- (x - b) / c
    ei <- exp(-zi^2 / 2)
    2 * v[["a"]] * v[["b"]] * zi / c * ei + 2 * v[["a"]] * v[["c"]] * zi^2 / c * ei - 
      v[["b"]]^2 * a / c^2 * (1 - zi^2) * ei - 2 * v[["b"]] * v[["c"]] * a / c^2 * zi * (2 - zi^2) * ei -
      v[["c"]]^2 * a / c^2 * zi^2 * (3 - zi^2) * ei
  })
}

## analytic fvv (1)
gsl_nls(
  fn = y ~ a * exp(-(x - b)^2 / (2 * c^2)), ## model formula
  data = data.frame(x = x, y = y),          ## model fit data
  start = c(a = 1, b = 0, c = 1),           ## starting values
  algorithm = "lmaccel",                    ## algorithm
  trace = TRUE,                             ## verbose output
  fvv = fvv,                                ## analytic function
  x = x                                     ## argument passed to fvv
)
#> iter   1: ssr = 158.14, par = (1.584, 0.502802, 0.512515)
#> iter   2: ssr = 126.579, par = (1.84317, 0.365984, 0.404378)
#> iter   3: ssr = 77.1032, par = (2.50015, 0.392468, 0.272532)
#> iter   4: ssr = 26.4382, par = (3.63788, 0.394722, 0.205505)
#> iter   5: ssr = 5.36705, par = (4.63344, 0.396903, 0.16368)
#> iter   6: ssr = 2.82578, par = (5.05546, 0.39791, 0.149341)
#> iter   7: ssr = 2.75877, par = (5.13243, 0.397896, 0.147057)
#> iter   8: ssr = 2.7583, par = (5.13862, 0.397885, 0.146843)
#> iter   9: ssr = 2.7583, par = (5.13893, 0.397884, 0.14683)
#> iter  10: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> iter  11: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> iter  12: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> *******************
#> summary from method 'multifit/levenberg-marquardt+accel'
#> number of iterations: 12
#> reason for stopping: input domain error
#> initial ssr = 210.146
#> final ssr = 2.7583
#> ssr/dof = 0.0586872
#> ssr achieved tolerance = 3.28626e-14
#> function evaluations: 58
#> jacobian evaluations: 0
#> fvv evaluations: 18
#> status = success
#> *******************
#> Nonlinear regression model
#>   model: y ~ a * exp(-(x - b)^2/(2 * c^2))
#>    data: data.frame(x = x, y = y)
#>      a      b      c 
#> 5.1389 0.3979 0.1468 
#>  residual sum-of-squares: 2.758
#> 
#> Algorithm: multifit/levenberg-marquardt+accel, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 12 
#> Achieved convergence tolerance: 3.286e-14

If the model formula fn can be derived with stats::deriv(), then the analytic Hessian and second directional derivatives in fvv can be computed automatically using symbolic differentiation. Analogous to the jac argument, to evaluate fvv by means of symbolic differentiation, set fvv = TRUE:

## analytic fvv (2)
gsl_nls(
  fn = y ~ a * exp(-(x - b)^2 / (2 * c^2)), ## model formula
  data = data.frame(x = x, y = y),          ## model fit data
  start = c(a = 1, b = 0, c = 1),           ## starting values
  algorithm = "lmaccel",                    ## algorithm
  trace = TRUE,                             ## verbose output
  fvv = TRUE                                ## automatic derivation
)
#> iter   1: ssr = 158.14, par = (1.584, 0.502802, 0.512515)
#> iter   2: ssr = 126.579, par = (1.84317, 0.365984, 0.404378)
#> iter   3: ssr = 77.1032, par = (2.50015, 0.392468, 0.272532)
#> iter   4: ssr = 26.4382, par = (3.63788, 0.394722, 0.205505)
#> iter   5: ssr = 5.36705, par = (4.63344, 0.396903, 0.16368)
#> iter   6: ssr = 2.82578, par = (5.05546, 0.39791, 0.149341)
#> iter   7: ssr = 2.75877, par = (5.13243, 0.397896, 0.147057)
#> iter   8: ssr = 2.7583, par = (5.13862, 0.397885, 0.146843)
#> iter   9: ssr = 2.7583, par = (5.13893, 0.397884, 0.14683)
#> iter  10: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> iter  11: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> iter  12: ssr = 2.7583, par = (5.13894, 0.397884, 0.146829)
#> *******************
#> summary from method 'multifit/levenberg-marquardt+accel'
#> number of iterations: 12
#> reason for stopping: input domain error
#> initial ssr = 210.146
#> final ssr = 2.7583
#> ssr/dof = 0.0586872
#> ssr achieved tolerance = 2.93099e-14
#> function evaluations: 58
#> jacobian evaluations: 0
#> fvv evaluations: 18
#> status = success
#> *******************
#> Nonlinear regression model
#>   model: y ~ a * exp(-(x - b)^2/(2 * c^2))
#>    data: data.frame(x = x, y = y)
#>      a      b      c 
#> 5.1389 0.3979 0.1468 
#>  residual sum-of-squares: 2.758
#> 
#> Algorithm: multifit/levenberg-marquardt+accel, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 12 
#> Achieved convergence tolerance: 2.931e-14

Example 3: Branin function

As a third example, we compare the available trust region methods by minimizing the Branin test function, a common optimization test problem. For the Branin test function, the following bivariate expression is used:

$\left\ \begin{aligned} F(x_1, x_2) & \= \f_1(x_1, x_2)^2 + f_2(x_1, x_2)^2 \ f_1(x_1, x_2) & \= \x_2 + a_1 x_1^2 + a_2 x_1 + a_3 \ f_2(x_1, x_2) & \= \\sqrt{a_4 \cdot (1 + (1 - a_5) \cos(x_1))} \end{aligned} \right.$

with known constants $a_1 = -5.1/(4 \pi^2)$ , $a_2 = 5/\pi$ , , , $a_5 = 1 / (8\pi)$ (cf. https://www.gnu.org/software/gsl/doc/html/nls.html#comparing-trs-methods-example), such that has three local minima in the range $(x_1, x_2) \in [-5, 15] \times [-5, 15]$ .

The minimization problem can be solved with gsl_nls() by considering the cost function as a sum of squared residuals in which and are two residuals relative to two zero responses. Here, instead of passing a formula to gsl_nls(), the nonlinear model is passed directly as a function. The first parameter of the function is the vector of parameters, i.e. , and the function returns the vector of model evaluations, i.e. . When passing a function instead of formula to gsl_nls(), the vector of observed responses should be included in the y argument. In this example, y is set to a vector of zeros. As starting values, we use and equivalent to the example in the GSL reference manual.

## Branin model function
branin <- function(x) {
  a <- c(-5.1 / (4 * pi^2), 5 / pi, -6, 10, 1 / (8 * pi))
  f1 <- x[2] + a[1] * x[1]^2 + a[2] * x[1] + a[3] 
  f2 <- sqrt(a[4] * (1 + (1 - a[5]) * cos(x[1])))
  c(f1, f2)
}

## Levenberg-Marquardt minimization
ex3_fit <- gsl_nls(
  fn = branin,                   ## model function      
  y = c(0, 0),                   ## response vector 
  start = c(x1 = 6, x2 = 14.5),  ## starting values
  algorithm = "lm"               ## algorithm
)

ex3_fit
#> Nonlinear regression model
#>   model: y ~ fn(x)
#>     x1     x2 
#> -3.142 12.275 
#>  residual sum-of-squares: 0.3979
#> 
#> Algorithm: multifit/levenberg-marquardt, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 20 
#> Achieved convergence tolerance: 0

Note: When using the function method of gsl_nls(), the returned object no longer has class "nls",

class(ex3_fit)
#> [1] "gsl_nls"

However, all generics anova, coef, confint, deviance, df.residual, fitted, formula, logLik, predict, print, residuals, summary, vcov and weights remain applicable to objects (only) of class "gls_nls".

Method comparisons

Solving the same minimization problem with all available trust region methods, i.e. algorithm set to "lm", "lmaccel", "dogleg", "ddogleg" and "subspace2D" respectively, and tracing the parameter values at each iteration, we can visualize the minimization paths followed by each method.

Analogous to the example in the GSL reference manual, the standard Levenberg-Marquardt method without geodesic acceleration converges to the minimum at $(-\pi, 12.275)$ , all other methods converge to the minimum at $(\pi, 2.275)$ .

Example 4: Large NLS example

To illustrate the use of gsl_nls_large(), we reproduce the large nonlinear least-squares example (https://www.gnu.org/software/gsl/doc/html/nls.html#large-nonlinear-least-squares-example) from the GSL reference manual. The nonlinear least squares model is defined as:

$\left\ \begin{aligned} f_i & \= \sqrt{\alpha}(\theta_i + 1), \quad i = 1,\ldots,p \ f_{p + 1} & \= \Vert \boldsymbol{\theta} \Vert^2 - \frac{1}{4} \end{aligned} \right.$

with given constant $\alpha = 10^{-5}$ and unknown parameters $\theta_1,\ldots, \theta_p$ . The residual $f_{p + 1}$ adds an -regularization constraint on the parameter vector and makes the model nonlinear. The $(p + 1) \times p$ -dimensional Jacobian matrix is given by:

$\boldsymbol{J}(\boldsymbol{\theta}) \= \ \left[ \begin{matrix} \frac{\partial f_1}{\partial \theta_1} & \ldots & \frac{\partial f_1}{\partial \theta_p} \ \vdots & \ddots & \vdots \ \frac{\partial f_{p+1}}{\partial \theta_1} & \ldots & \frac{\partial f_{p+1}}{\partial \theta_p} \end{matrix} \right] \= \left[ \begin{matrix} \sqrt{\alpha} \boldsymbol{I}_{p \times p} \ 2 \boldsymbol{\theta}' \end{matrix} \right]$

with $\boldsymbol{I}_{p \times p}$ the $(p \times p)$ -dimensional identity matrix.

The model residuals and Jacobian matrix can be written as a function of the parameter vector $\boldsymbol{\theta}$ as,

## model and jacobian
f <- function(theta) {
  val <- c(sqrt(1e-5) * (theta - 1), sum(theta^2) - 0.25)
  attr(val, "gradient") <- rbind(diag(sqrt(1e-5), nrow = length(theta)), 2 * t(theta))
  return(val)
}

Here, the Jacobian is returned in the "gradient" attribute of the evaluated vector (as in a selfStart model) from which it is detected automatically by gsl_nls() or gsl_nls_large().

First, the least squares objective is minimized with a call to gsl_nls() analogous to the previous example by passing the nonlinear model as a function and setting the response vector y to a vector of zeros. The number of parameters is set to and as starting values we use $\theta_1 = 1, \ldots, \theta_p = p$ equivalent to the example in the GSL reference manual.

## number of parameters
p <- 500

## standard Levenberg-Marquardt
system.time({ 
  ex4_fit_lm <- gsl_nls(
    fn = f,
    y = rep(0, p + 1),
    start = 1:p,
    control = list(maxiter = 500)
  )
})
#>    user  system elapsed 
#>  33.720   0.084  33.812

cat("Residual sum-of-squares:", deviance(ex4_fit_lm), "\n")
#> Residual sum-of-squares: 0.004778845

Second, the same model is fitted with a call to gsl_nls_large() using the Steihaug-Toint Conjugate Gradient algorithm, which results in a much smaller runtime:

## large-scale Steihaug-Toint 
system.time({ 
  ex4_fit_cgst <- gsl_nls_large(
    fn = f,
    y = rep(0, p + 1),
    start = 1:p,
    algorithm = "cgst",
    control = list(maxiter = 500)
  )
})
#>    user  system elapsed 
#>   1.214   0.312   1.527

cat("Residual sum-of-squares:", deviance(ex4_fit_cgst), "\n")
#> Residual sum-of-squares: 0.004778845

Sparse Jacobian matrix

The Jacobian matrix $\boldsymbol{J}(\boldsymbol{\theta})$ is very sparse in the sense that it contains only a small number of nonzero entries. The gsl_nls_large() function also accepts the calculated Jacobian as a sparse matrix of class "dgCMatrix", "dgRMatrix" or "dgTMatrix" (see the Matrix package). The following updated model function returns the sparse Jacobian as a "dgCMatrix" instead of a dense numeric matrix:

## model and sparse Jacobian
fsp <- function(theta) {
  val <- c(sqrt(1e-5) * (theta - 1), sum(theta^2) - 0.25)
  attr(val, "gradient") <- rbind(Matrix::Diagonal(x = sqrt(1e-5), n = length(theta)), 2 * t(theta))
  return(val)
}

As illustrated by the benchmarks below, besides a slight improvement in runtimes, the required amount of memory is significantly smaller for the model functions returning a sparse Jacobian than the model functions returning a dense Jacobian:

## computation times and allocated memory
bench::mark(
  "Dense LM" = gsl_nls_large(fn = f, y = rep(0, p + 1), start = 1:p, algorithm = "lm", control = list(maxiter = 500)),
  "Dense CGST" = gsl_nls_large(fn = f, y = rep(0, p + 1), start = 1:p, algorithm = "cgst"),
  "Sparse LM" = gsl_nls_large(fn = fsp, y = rep(0, p + 1), start = 1:p, algorithm = "lm", control = list(maxiter = 500)),
  "Sparse CGST" = gsl_nls_large(fn = fsp, y = rep(0, p + 1), start = 1:p, algorithm = "cgst"),
  check = FALSE,
  min_iterations = 5
)
#> # A tibble: 4 × 6
#>   expression       min   median `itr/sec` mem_alloc `gc/sec`
#>   <bch:expr>  <bch:tm> <bch:tm>     <dbl> <bch:byt>    <dbl>
#> 1 Dense LM       6.33s    6.39s     0.157     1.8GB    6.61  
#> 2 Dense CGST     1.29s    1.36s     0.726    1.02GB    16.4  
#> 3 Sparse LM      4.87s    4.91s     0.203   33.19MB    0.122
#> 4 Sparse CGST 166.09ms 176.09ms     4.66    23.04MB    3.73

NLS test problems

The R-package currently contains a collection of 59 NLS test problems originating primarily from the NIST Statistical Reference Datasets (StRD) archive; Bates and Watts (1988); and Moré, Garbow, and Hillstrom (1981).

## avalable test problems
nls_test_list()
#>                                     name    class  p   n       check
#> 1                                Misra1a  formula  2  14  p, n fixed
#> 2                               Chwirut2  formula  3  54  p, n fixed
#> 3                               Chwirut1  formula  3 214  p, n fixed
#> 4                               Lanczos3  formula  6  24  p, n fixed
#> 5                                 Gauss1  formula  8 250  p, n fixed
#> 6                                 Gauss2  formula  8 250  p, n fixed
#> 7                                DanWood  formula  2   6  p, n fixed
#> 8                                Misra1b  formula  2  14  p, n fixed
#> 9                                 Kirby2  formula  5 151  p, n fixed
#> 10                                 Hahn1  formula  7 236  p, n fixed
#> 11                                Nelson  formula  3 128  p, n fixed
#> 12                                 MGH17  formula  5  33  p, n fixed
#> 13                              Lanczos1  formula  6  24  p, n fixed
#> 14                              Lanczos2  formula  6  24  p, n fixed
#> 15                                Gauss3  formula  8 250  p, n fixed
#> 16                               Misra1c  formula  2  14  p, n fixed
#> 17                               Misra1d  formula  2  14  p, n fixed
#> 18                              Roszman1  formula  4  25  p, n fixed
#> 19                                  ENSO  formula  9 168  p, n fixed
#> 20                                 MGH09  formula  4  11  p, n fixed
#> 21                               Thurber  formula  7  37  p, n fixed
#> 22                                BoxBOD  formula  2   6  p, n fixed
#> 23                            Ratkowsky2  formula  3   9  p, n fixed
#> 24                                 MGH10  formula  3  16  p, n fixed
#> 25                              Eckerle4  formula  3  35  p, n fixed
#> 26                            Ratkowsky3  formula  4  15  p, n fixed
#> 27                              Bennett5  formula  3 154  p, n fixed
#> 28                         Isomerization  formula  4  24  p, n fixed
#> 29                             Lubricant  formula  9  53  p, n fixed
#> 30                         Sulfisoxazole  formula  4  12  p, n fixed
#> 31                                Leaves  formula  4  15  p, n fixed
#> 32                              Chloride  formula  3  54  p, n fixed
#> 33                          Tetracycline  formula  4   9  p, n fixed
#> 34                     Linear, full rank function  5  10 p <= n free
#> 35                        Linear, rank 1 function  5  10 p <= n free
#> 36 Linear, rank 1, zero columns and rows function  5  10 p <= n free
#> 37                            Rosenbrock function  2   2  p, n fixed
#> 38                        Helical valley function  3   3  p, n fixed
#> 39                       Powell singular function  4   4  p, n fixed
#> 40                     Freudenstein/Roth function  2   2  p, n fixed
#> 41                                  Bard function  3  15  p, n fixed
#> 42                   Kowalik and Osborne function  4  11  p, n fixed
#> 43                                 Meyer function  3  16  p, n fixed
#> 44                                Watson function  6  31  p, n fixed
#> 45                     Box 3-dimensional function  3  10 p <= n free
#> 46                  Jennrich and Sampson function  2  10 p <= n free
#> 47                      Brown and Dennis function  4  20 p <= n free
#> 48                             Chebyquad function  9   9 p <= n free
#> 49                   Brown almost-linear function 10  10 p == n free
#> 50                             Osborne 1 function  5  33  p, n fixed
#> 51                             Osborne 2 function 11  65  p, n fixed
#> 52                              Hanson 1 function  2  16  p, n fixed
#> 53                              Hanson 2 function  3  16  p, n fixed
#> 54                             McKeown 1 function  2   3  p, n fixed
#> 55                             McKeown 2 function  3   4  p, n fixed
#> 56                             McKeown 3 function  5  10  p, n fixed
#> 57              Devilliers and Glasser 1 function  4  24  p, n fixed
#> 58              Devilliers and Glasser 2 function  5  16  p, n fixed
#> 59                        Madsen example function  2   3  p, n fixed

The function nls_test_problem() fetches the model definition and model data required to solve a specific NLS test problem with gsl_nls() (or nls() if the model is defined as a formula). This also returns the vector of certified target values corresponding to the best-available solutions and a vector of suggested starting values for the parameters:

## example regression problem
(ratkowsky2 <- nls_test_problem(name = "Ratkowsky2"))
#> $data
#>       y  x
#> 1  8.93  9
#> 2 10.80 14
#> 3 18.59 21
#> 4 22.33 28
#> 5 39.35 42
#> 6 56.11 57
#> 7 61.73 63
#> 8 64.62 70
#> 9 67.08 79
#> 
#> $fn
#> y ~ b1/(1 + exp(b2 - b3 * x))
#> <environment: 0x55b96bf04da0>
#> 
#> $start
#>    b1    b2    b3 
#> 100.0   1.0   0.1 
#> 
#> $target
#>         b1         b2         b3 
#> 72.4622376  2.6180768  0.0673592 
#> 
#> attr(,"class")
#> [1] "nls_test_formula"

with(ratkowsky2,
     gsl_nls(
       fn = fn,
       data = data,
       start = start
     )
)
#> Nonlinear regression model
#>   model: y ~ b1/(1 + exp(b2 - b3 * x))
#>    data: data
#>       b1       b2       b3 
#> 72.46224  2.61808  0.06736 
#>  residual sum-of-squares: 8.057
#> 
#> Algorithm: multifit/levenberg-marquardt, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 10 
#> Achieved convergence tolerance: 4.619e-14

## example optimization problem
madsen <- nls_test_problem(name = "Madsen")
with(madsen,
     gsl_nls(
       fn = fn,
       y = y,
       start = start,
       jac = jac
     )
)
#> Nonlinear regression model
#>   model: y ~ fn(x)
#>      x1      x2 
#> -0.1554  0.6946 
#>  residual sum-of-squares: 0.7732
#> 
#> Algorithm: multifit/levenberg-marquardt, (scaling: more, solver: qr)
#> 
#> Number of iterations to convergence: 42 
#> Achieved convergence tolerance: 1.11e-16

Other R-packages

Other CRAN R-packages interfacing with GSL that served as inspiration for this package include:

RcppGSL by Dirk Eddelbuettel and Romain Francois
GSL by Robin Hankin and others
RcppZiggurat by Dirk Eddelbuettel

References

Bates, D.M., and D.G. Watts. 1988. Nonlinear Regression Analysis and Its Applications ISBN 0471816434.

Galassi, M., J. Davies, J. Theiler, B. Gough, G. Jungman, M. Booth, and F. Rossi. 2009. GNU Scientific Library Reference Manual (3rd Ed.), ISBN 0954612078. https://www.gnu.org/software/gsl/.

Hickernell, F.J., and Y. Yuan. 1997. “A Simple Multistart Algorithm for Global Optimization.” OR Transactions 1(2).

Moré, J.J., B.S. Garbow, and K.E. Hillstrom. 1981. “Testing Unconstrained Optimization Software.” ACM Transactions on Mathematical Software (TOMS) 7(1).

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.Rbuildignore		.Rbuildignore
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NAMESPACE		NAMESPACE
NEWS.md		NEWS.md
README.md		README.md
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{gslnls}: GSL Multi-Start Nonlinear Least-Squares Fitting in R

Installation from source

System requirements

GSL installation examples

Ubuntu, Debian

macOS

Fedora, RedHat, CentOS

Windows

R-package installation

Installation from binary

Example usage

Example 1: Exponential model

Data

Model fit

Object methods

Jacobian calculation

Multi-start optimization

Example 2: Gaussian function

Data

Model fit

Geodesic acceleration

Second directional derivative

Example 3: Branin function

Method comparisons

Example 4: Large NLS example

Sparse Jacobian matrix

NLS test problems

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{gslnls}: GSL Multi-Start Nonlinear Least-Squares Fitting in R

Installation from source

System requirements

GSL installation examples

Ubuntu, Debian

macOS

Fedora, RedHat, CentOS

Windows

R-package installation

Installation from binary

Example usage

Example 1: Exponential model

Data

Model fit

Object methods

Jacobian calculation

Multi-start optimization

Example 2: Gaussian function

Data

Model fit

Geodesic acceleration

Second directional derivative

Example 3: Branin function

Method comparisons

Example 4: Large NLS example

Sparse Jacobian matrix

NLS test problems

Other R-packages

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