
R version 3.5.0 Patched (2018-04-30 r74685) -- "Joy in Playing"
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> #  File src/library/stats/tests/nls.R
> #  Part of the R package, https://www.R-project.org
> #
> #  This program is free software; you can redistribute it and/or modify
> #  it under the terms of the GNU General Public License as published by
> #  the Free Software Foundation; either version 2 of the License, or
> #  (at your option) any later version.
> #
> #  This program is distributed in the hope that it will be useful,
> #  but WITHOUT ANY WARRANTY; without even the implied warranty of
> #  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
> #  GNU General Public License for more details.
> #
> #  A copy of the GNU General Public License is available at
> #  https://www.R-project.org/Licenses/
> 
> ## tests of nls, especially of weighted fits
> 
> library(stats)
> options(digits = 5) # to avoid trivial printed differences
> options(useFancyQuotes = FALSE) # avoid fancy quotes in o/p
> options(show.nls.convergence = FALSE) # avoid non-diffable output
> options(warn = 1)
> 
> have_MASS <- requireNamespace('MASS', quietly = TRUE)
> 
> pdf("nls-test.pdf")
> 
> ## utility for comparing nls() results:  [TODO: use more often below]
> .n <- function(r) r[names(r) != "call"]
> 
> ## selfStart.default() w/ no parameters:
> logist <- deriv( ~Asym/(1+exp(-(x-xmid)/scal)), c("Asym", "xmid", "scal"),
+ 		function(x, Asym, xmid, scal){} )
> logistInit <- function(mCall, LHS, data) {
+     xy <- sortedXyData(mCall[["x"]], LHS, data)
+     if(nrow(xy) < 3) stop("Too few distinct input values to fit a logistic")
+     Asym <- max(abs(xy[,"y"]))
+     if (Asym != max(xy[,"y"])) Asym <- -Asym  # negative asymptote
+     xmid <- NLSstClosestX(xy, 0.5 * Asym)
+     scal <- NLSstClosestX(xy, 0.75 * Asym) - xmid
+     setNames(c(Asym, xmid, scal),
+ 	     mCall[c("Asym", "xmid", "scal")])
+ }
> logist <- selfStart(logist, initial = logistInit) ##-> Error in R 1.5.0
> str(logist)
function (x, Asym, xmid, scal)  
 - attr(*, "initial")=function (mCall, LHS, data)  
 - attr(*, "class")= chr "selfStart"
> 
> ## lower and upper in algorithm="port"
> set.seed(123)
> x <- runif(200)
> a <- b <- 1; c <- -0.1
> y <- a+b*x+c*x^2+rnorm(200, sd=0.05)
> plot(x,y)
> curve(a+b*x+c*x^2, add = TRUE)
> nls(y ~ a+b*x+c*I(x^2), start = c(a=1, b=1, c=0.1), algorithm = "port")
Nonlinear regression model
  model: y ~ a + b * x + c * I(x^2)
   data: parent.frame()
      a       b       c 
 1.0058  0.9824 -0.0897 
 residual sum-of-squares: 0.46

Algorithm "port", convergence message: relative convergence (4)
> (fm <- nls(y ~ a+b*x+c*I(x^2), start = c(a=1, b=1, c=0.1),
+            algorithm = "port", lower = c(0, 0, 0)))
Nonlinear regression model
  model: y ~ a + b * x + c * I(x^2)
   data: parent.frame()
   a    b    c 
1.02 0.89 0.00 
 residual sum-of-squares: 0.468

Algorithm "port", convergence message: both X-convergence and relative convergence (5)
> if(have_MASS) print(confint(fm))
Waiting for profiling to be done...
     2.5%    97.5%
a 1.00875 1.037847
b 0.84138 0.914645
c      NA 0.042807
> 
> ## weighted nls fit: unsupported < 2.3.0
> set.seed(123)
> y <- x <- 1:10
> yeps <- y + rnorm(length(y), sd = 0.01)
> wts <- rep(c(1, 2), length = 10); wts[5] <- 0
> fit0 <- lm(yeps ~ x, weights = wts)
> summary(fit0, cor = TRUE)

Call:
lm(formula = yeps ~ x, weights = wts)

Weighted Residuals:
     Min       1Q   Median       3Q      Max 
-0.01562 -0.00723 -0.00158  0.00403  0.02413 

Coefficients:
            Estimate Std. Error t value Pr(>|t|)    
(Intercept)  0.00517    0.00764    0.68     0.52    
x            0.99915    0.00119  841.38   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.0132 on 7 degrees of freedom
Multiple R-squared:     1,	Adjusted R-squared:     1 
F-statistic: 7.08e+05 on 1 and 7 DF,  p-value: <2e-16

Correlation of Coefficients:
  (Intercept)
x -0.89      

> cf0 <- coef(summary(fit0))[, 1:2]
> fit <- nls(yeps ~ a + b*x, start = list(a = 0.12345, b = 0.54321),
+            weights = wts, trace = TRUE)
112.14 :  0.12345 0.54321
0.0012128 :  0.0051705 0.9991529
> summary(fit, cor = TRUE)

Formula: yeps ~ a + b * x

Parameters:
  Estimate Std. Error t value Pr(>|t|)    
a  0.00517    0.00764    0.68     0.52    
b  0.99915    0.00119  841.37   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.0132 on 7 degrees of freedom

Correlation of Parameter Estimates:
  a    
b -0.89

> stopifnot(all.equal(residuals(fit), residuals(fit0), tolerance = 1e-5,
+                     check.attributes = FALSE))
> stopifnot(df.residual(fit) == df.residual(fit0))
> cf1 <- coef(summary(fit))[, 1:2]
> fit2 <- nls(yeps ~ a + b*x, start = list(a = 0.12345, b = 0.54321),
+             weights = wts, trace = TRUE, algorithm = "port")
  0:     56.070572: 0.123450 0.543210
  1:     6.3964587:  1.34546 0.700840
  2: 0.00060639084: 0.00517053 0.999153
  3: 0.00060639084: 0.00517051 0.999153
> summary(fit2, cor = TRUE)

Formula: yeps ~ a + b * x

Parameters:
  Estimate Std. Error t value Pr(>|t|)    
a  0.00517    0.00764    0.68     0.52    
b  0.99915    0.00119  841.38   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.0132 on 7 degrees of freedom

Correlation of Parameter Estimates:
  a    
b -0.89

Algorithm "port", convergence message: both X-convergence and relative convergence (5)

> cf2 <- coef(summary(fit2))[, 1:2]
> rownames(cf0) <- c("a", "b")
> # expect relative errors ca 2e-08
> stopifnot(all.equal(cf1, cf0, tolerance = 1e-6),
+           all.equal(cf1, cf0, tolerance = 1e-6))
> stopifnot(all.equal(residuals(fit2), residuals(fit0), tolerance = 1e5,
+                     check.attributes = FALSE))
> 
> 
> DNase1 <- subset(DNase, Run == 1)
> DNase1$wts <- rep(8:1, each = 2)
> fm1 <- nls(density ~ SSlogis(log(conc), Asym, xmid, scal),
+            data = DNase1, weights = wts)
> summary(fm1)

Formula: density ~ SSlogis(log(conc), Asym, xmid, scal)

Parameters:
     Estimate Std. Error t value Pr(>|t|)    
Asym   2.3350     0.0966    24.2  3.5e-12 ***
xmid   1.4731     0.0947    15.6  8.8e-10 ***
scal   1.0385     0.0304    34.1  4.2e-14 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.0355 on 13 degrees of freedom

> 
> ## directly
> fm2 <- nls(density ~ Asym/(1 + exp((xmid - log(conc))/scal)),
+            data = DNase1, weights = wts,
+            start = list(Asym = 3, xmid = 0, scal = 1))
> summary(fm2)

Formula: density ~ Asym/(1 + exp((xmid - log(conc))/scal))

Parameters:
     Estimate Std. Error t value Pr(>|t|)    
Asym   2.3350     0.0966    24.2  3.5e-12 ***
xmid   1.4731     0.0947    15.6  8.8e-10 ***
scal   1.0385     0.0304    34.1  4.2e-14 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.0355 on 13 degrees of freedom

> stopifnot(all.equal(coef(summary(fm2)), coef(summary(fm1)), tolerance = 1e-6))
> stopifnot(all.equal(residuals(fm2), residuals(fm1), tolerance = 1e-5))
> stopifnot(all.equal(fitted(fm2), fitted(fm1), tolerance = 1e-6))
> fm2a <- nls(density ~ Asym/(1 + exp((xmid - log(conc)))),
+             data = DNase1, weights = wts,
+             start = list(Asym = 3, xmid = 0))
> anova(fm2a, fm2)
Analysis of Variance Table

Model 1: density ~ Asym/(1 + exp((xmid - log(conc))))
Model 2: density ~ Asym/(1 + exp((xmid - log(conc))/scal))
  Res.Df Res.Sum Sq Df  Sum Sq F value Pr(>F)
1     14     0.0186                          
2     13     0.0164  1 0.00212    1.68   0.22
> 
> ## and without using weights
> fm3 <- nls(~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc))/scal))),
+            data = DNase1, start = list(Asym = 3, xmid = 0, scal = 1))
> summary(fm3)

Formula: 0 ~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc))/scal)))

Parameters:
     Estimate Std. Error t value Pr(>|t|)    
Asym   2.3350     0.0966    24.2  3.5e-12 ***
xmid   1.4731     0.0947    15.6  8.8e-10 ***
scal   1.0385     0.0304    34.1  4.2e-14 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.0355 on 13 degrees of freedom

> stopifnot(all.equal(coef(summary(fm3)), coef(summary(fm1)), tolerance = 1e-6))
> ft <- with(DNase1, density - fitted(fm3)/sqrt(wts))
> stopifnot(all.equal(ft, fitted(fm1), tolerance = 1e-6))
> # sign of residuals is reversed
> r <- with(DNase1, -residuals(fm3)/sqrt(wts))
> all.equal(r, residuals(fm1), tolerance = 1e-5)
[1] TRUE
> fm3a <- nls(~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc))))),
+             data = DNase1, start = list(Asym = 3, xmid = 0))
> anova(fm3a, fm3)
Analysis of Variance Table

Model 1: 0 ~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc)))))
Model 2: 0 ~ sqrt(wts) * (density - Asym/(1 + exp((xmid - log(conc))/scal)))
  Res.Df Res.Sum Sq Df  Sum Sq F value Pr(>F)
1     14     0.0186                          
2     13     0.0164  1 0.00212    1.68   0.22
> 
> ## using conditional linearity
> fm4 <- nls(density ~ 1/(1 + exp((xmid - log(conc))/scal)),
+            data = DNase1, weights = wts,
+            start = list(xmid = 0, scal = 1), algorithm = "plinear")
> summary(fm4)

Formula: density ~ 1/(1 + exp((xmid - log(conc))/scal))

Parameters:
     Estimate Std. Error t value Pr(>|t|)    
xmid   1.4731     0.0947    15.6  8.8e-10 ***
scal   1.0385     0.0304    34.1  4.2e-14 ***
.lin   2.3350     0.0966    24.2  3.5e-12 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.0355 on 13 degrees of freedom

> cf <- coef(summary(fm4))[c(3,1,2), ]
> rownames(cf)[2] <- "Asym"
> stopifnot(all.equal(cf, coef(summary(fm1)), tolerance = 1e-6,
+                     check.attributes = FALSE))
> stopifnot(all.equal(residuals(fm4), residuals(fm1), tolerance = 1e-5))
> stopifnot(all.equal(fitted(fm4), fitted(fm1), tolerance = 1e-6))
> fm4a <- nls(density ~ 1/(1 + exp((xmid - log(conc)))),
+             data = DNase1, weights = wts,
+             start = list(xmid = 0), algorithm = "plinear")
> anova(fm4a, fm4)
Analysis of Variance Table

Model 1: density ~ 1/(1 + exp((xmid - log(conc))))
Model 2: density ~ 1/(1 + exp((xmid - log(conc))/scal))
  Res.Df Res.Sum Sq Df  Sum Sq F value Pr(>F)
1     14     0.0186                          
2     13     0.0164  1 0.00212    1.68   0.22
> 
> ## using 'port'
> fm5 <- nls(density ~ Asym/(1 + exp((xmid - log(conc))/scal)),
+            data = DNase1, weights = wts,
+            start = list(Asym = 3, xmid = 0, scal = 1),
+            algorithm = "port")
> summary(fm5)

Formula: density ~ Asym/(1 + exp((xmid - log(conc))/scal))

Parameters:
     Estimate Std. Error t value Pr(>|t|)    
Asym   2.3350     0.0966    24.2  3.5e-12 ***
xmid   1.4731     0.0947    15.6  8.8e-10 ***
scal   1.0385     0.0304    34.1  4.2e-14 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.0355 on 13 degrees of freedom

Algorithm "port", convergence message: relative convergence (4)

> stopifnot(all.equal(coef(summary(fm5)), coef(summary(fm1)), tolerance = 1e-6))
> stopifnot(all.equal(residuals(fm5), residuals(fm1), tolerance = 1e-5))
> stopifnot(all.equal(fitted(fm5), fitted(fm1), tolerance = 1e-6))
> 
> ## check profiling
> pfm1 <- profile(fm1)
> pfm3 <- profile(fm3)
> for(m in names(pfm1))
+     stopifnot(all.equal(pfm1[[m]], pfm3[[m]], tolerance = 1e-5))
> pfm5 <- profile(fm5)
> for(m in names(pfm1))
+     stopifnot(all.equal(pfm1[[m]], pfm5[[m]], tolerance = 1e-5))
> if(have_MASS) {
+     print(c1 <- confint(fm1))
+     print(c4 <- confint(fm4, 1:2))
+     stopifnot(all.equal(c1[2:3, ], c4, tolerance = 1e-3))
+ }
Waiting for profiling to be done...
        2.5%  97.5%
Asym 2.14936 2.5724
xmid 1.28535 1.6966
scal 0.97526 1.1068
Waiting for profiling to be done...
       2.5%  97.5%
xmid 1.2866 1.6949
scal 0.9757 1.1063
> 
> ## some low-dimensional examples
> npts <- 1000
> set.seed(1001)
> x <- runif(npts)
> b <- 0.7
> y <- x^b+rnorm(npts, sd=0.05)
> a <- 0.5
> y2 <- a*x^b+rnorm(npts, sd=0.05)
> c <- 1.0
> y3 <- a*(x+c)^b+rnorm(npts, sd=0.05)
> d <- 0.5
> y4 <- a*(x^d+c)^b+rnorm(npts, sd=0.05)
> m1 <- c(y ~ x^b, y2 ~ a*x^b, y3 ~ a*(x+exp(logc))^b)
> s1 <- list(c(b=1), c(a=1,b=1), c(a=1,b=1,logc=0))
> for(p in 1:3) {
+     fm <- nls(m1[[p]], start = s1[[p]])
+     print(fm)
+     if(have_MASS) print(confint(fm))
+     fm <- nls(m1[[p]], start = s1[[p]], algorithm = "port")
+     print(fm)
+     if(have_MASS) print(confint(fm))
+ }
Nonlinear regression model
  model: y ~ x^b
   data: parent.frame()
    b 
0.695 
 residual sum-of-squares: 2.39
Waiting for profiling to be done...
   2.5%   97.5% 
0.68704 0.70281 
Nonlinear regression model
  model: y ~ x^b
   data: parent.frame()
    b 
0.695 
 residual sum-of-squares: 2.39

Algorithm "port", convergence message: relative convergence (4)
Waiting for profiling to be done...
   2.5%   97.5% 
0.68704 0.70281 
Nonlinear regression model
  model: y2 ~ a * x^b
   data: parent.frame()
    a     b 
0.502 0.724 
 residual sum-of-squares: 2.51
Waiting for profiling to be done...
     2.5%   97.5%
a 0.49494 0.50893
b 0.70019 0.74767
Nonlinear regression model
  model: y2 ~ a * x^b
   data: parent.frame()
    a     b 
0.502 0.724 
 residual sum-of-squares: 2.51

Algorithm "port", convergence message: relative convergence (4)
Waiting for profiling to be done...
     2.5%   97.5%
a 0.49494 0.50893
b 0.70019 0.74767
Nonlinear regression model
  model: y3 ~ a * (x + exp(logc))^b
   data: parent.frame()
     a      b   logc 
 0.558  0.603 -0.176 
 residual sum-of-squares: 2.44
Waiting for profiling to be done...
         2.5%   97.5%
a     0.35006 0.66057
b     0.45107 0.91473
logc -0.64627 0.40946
Nonlinear regression model
  model: y3 ~ a * (x + exp(logc))^b
   data: parent.frame()
     a      b   logc 
 0.558  0.603 -0.176 
 residual sum-of-squares: 2.44

Algorithm "port", convergence message: relative convergence (4)
Waiting for profiling to be done...
         2.5%   97.5%
a     0.35006 0.66057
b     0.45107 0.91473
logc -0.64627 0.40946
> 
> if(have_MASS) {
+     fm <- nls(y2~x^b, start=c(b=1), algorithm="plinear")
+     print(confint(profile(fm)))
+     fm <- nls(y3 ~ (x+exp(logc))^b, start=c(b=1, logc=0), algorithm="plinear")
+     print(confint(profile(fm)))
+ }
   2.5%   97.5% 
0.70019 0.74767 
         2.5%   97.5%
b     0.45105 0.91471
logc -0.64625 0.40933
> 
> 
> ## more profiling with bounds
> op <- options(digits=3)
> npts <- 10
> set.seed(1001)
> a <- 2
> b <- 0.5
> x <- runif(npts)
> y <- a*x/(1+a*b*x) + rnorm(npts, sd=0.2)
> gfun <- function(a,b,x) {
+     if(a < 0 || b < 0) stop("bounds violated")
+     a*x/(1+a*b*x)
+ }
> m1 <- nls(y ~ gfun(a,b,x), algorithm = "port",
+           lower = c(0,0), start = c(a=1, b=1))
> (pr1 <- profile(m1))
$a
      tau par.vals.a par.vals.b
1  -3.869      0.706      0.000
2  -3.114      0.802      0.000
3  -0.863      1.124      0.000
4   0.000      1.538      0.263
5   0.590      1.952      0.446
6   1.070      2.423      0.592
7   1.534      3.082      0.737
8   1.969      4.034      0.878
9   2.376      5.502      1.014
10  2.751      7.929      1.144
11  3.090     12.263      1.264
12  3.375     20.845      1.373

$b
     tau par.vals.a par.vals.b
1 -0.673     1.2087     0.0272
2  0.000     1.5381     0.2633
3  0.707     2.0026     0.4994
4  1.365     2.6295     0.7236
5  1.994     3.5762     0.9522
6  2.611     5.1820     1.1962
7  3.225     8.2162     1.4614
8  3.820    17.3946     1.7512

attr(,"original.fit")
Nonlinear regression model
  model: y ~ gfun(a, b, x)
   data: parent.frame()
    a     b 
1.538 0.263 
 residual sum-of-squares: 0.389

Algorithm "port", convergence message: relative convergence (4)
attr(,"summary")

Formula: y ~ gfun(a, b, x)

Parameters:
  Estimate Std. Error t value Pr(>|t|)  
a    1.538      0.617    2.49    0.037 *
b    0.263      0.352    0.75    0.476  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.221 on 8 degrees of freedom

Algorithm "port", convergence message: relative convergence (4)

attr(,"class")
[1] "profile.nls" "profile"    
> if(have_MASS) print(confint(pr1))
  2.5% 97.5%
a 0.96  5.20
b   NA  1.07
> 
> gfun <- function(a,b,x) {
+     if(a < 0 || b < 0 || a > 1.5 || b > 1) stop("bounds violated")
+     a*x/(1+a*b*x)
+ }
> m2 <- nls(y ~ gfun(a,b,x), algorithm = "port",
+           lower = c(0, 0), upper=c(1.5, 1), start = c(a=1, b=1))
> profile(m2)
$a
     tau par.vals.a par.vals.b
1 -3.681      0.729      0.000
2 -2.945      0.823      0.000
3 -0.977      1.099      0.000
4  0.000      1.500      0.243

$b
     tau par.vals.a par.vals.b
1 -0.733    1.18200    0.00395
2  0.000    1.50000    0.24263
3  1.645    1.50000    0.48132
4  2.154    1.50000    0.57869
5  2.727    1.50000    0.70706
6  3.288    1.50000    0.85748

attr(,"original.fit")
Nonlinear regression model
  model: y ~ gfun(a, b, x)
   data: parent.frame()
    a     b 
1.500 0.243 
 residual sum-of-squares: 0.39

Algorithm "port", convergence message: relative convergence (4)
attr(,"summary")

Formula: y ~ gfun(a, b, x)

Parameters:
  Estimate Std. Error t value Pr(>|t|)  
a    1.500      0.598    2.51    0.036 *
b    0.243      0.356    0.68    0.514  
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.221 on 8 degrees of freedom

Algorithm "port", convergence message: relative convergence (4)

attr(,"class")
[1] "profile.nls" "profile"    
> if(have_MASS) print(confint(m2))
Waiting for profiling to be done...
   2.5% 97.5%
a 0.907    NA
b    NA 0.611
> options(op)
> 
> ## scoping problems
> test <- function(trace=TRUE)
+ {
+     x <- seq(0,5,len=20)
+     n <- 1
+     y <- 2*x^2 + n + rnorm(x)
+     xy <- data.frame(x=x,y=y)
+     myf <- function(x,a,b,c) a*x^b+c
+     list(with.start=
+          nls(y ~ myf(x,a,b,n), data=xy, start=c(a=1,b=1), trace=trace),
+          no.start= ## cheap auto-init to 1
+ 	 suppressWarnings(
+ 	     nls(y ~ myf(x,A,B,n), data=xy)))
+ }
> t1 <- test(); t1$with.start
8291.9 :  1 1
726.02 :  0.80544 2.42971
552.85 :  1.290 2.129
70.431 :  1.9565 1.9670
26.555 :  1.9788 2.0064
26.503 :  1.9798 2.0046
26.503 :  1.9799 2.0046
Nonlinear regression model
  model: y ~ myf(x, a, b, n)
   data: xy
   a    b 
1.98 2.00 
 residual sum-of-squares: 26.5
> ##__with.start:
> ## failed to find n in 2.2.x
> ## found wrong n in 2.3.x
> ## finally worked in 2.4.0
> ##__no.start: failed in 3.0.2
> stopifnot(all.equal(.n(t1[[1]]), .n(t1[[2]])))
> rm(a,b)
> t2 <- test(FALSE)
> stopifnot(all.equal(lapply(t1, .n),
+ 		    lapply(t2, .n), tolerance = 0.16))# different random error
> 
> 
> ## list 'start'
> set.seed(101)# (remain independent of above)
> getExpmat <- function(theta, t)
+ {
+         conc <- matrix(nrow = length(t), ncol = length(theta))
+         for(i in 1:length(theta)) conc[, i] <- exp(-theta[i] * t)
+         conc
+ }
> expsum <- as.vector(getExpmat(c(.05,.005), 1:100) %*% c(1,1))
> expsumNoisy <- expsum + max(expsum) *.001 * rnorm(100)
> expsum.df <-data.frame(expsumNoisy)
> 
> ## estimate decay rates, amplitudes with default Gauss-Newton
> summary (nls(expsumNoisy ~ getExpmat(k, 1:100) %*% sp, expsum.df,
+              start = list(k = c(.6,.02), sp = c(1,2))))

Formula: expsumNoisy ~ getExpmat(k, 1:100) %*% sp

Parameters:
    Estimate Std. Error t value Pr(>|t|)    
k1  5.00e-02   2.73e-04     183   <2e-16 ***
k2  4.97e-03   4.77e-05     104   <2e-16 ***
sp1 1.00e+00   3.96e-03     253   <2e-16 ***
sp2 9.98e-01   4.43e-03     225   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.00182 on 96 degrees of freedom

> 
> ## didn't work with port in 2.4.1
> summary (nls(expsumNoisy ~ getExpmat(k, 1:100) %*% sp, expsum.df,
+              start = list(k = c(.6,.02), sp = c(1,2)),
+              algorithm = "port"))

Formula: expsumNoisy ~ getExpmat(k, 1:100) %*% sp

Parameters:
    Estimate Std. Error t value Pr(>|t|)    
k1  5.00e-02   2.73e-04     183   <2e-16 ***
k2  4.97e-03   4.77e-05     104   <2e-16 ***
sp1 1.00e+00   3.96e-03     253   <2e-16 ***
sp2 9.98e-01   4.43e-03     225   <2e-16 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.00182 on 96 degrees of freedom

Algorithm "port", convergence message: both X-convergence and relative convergence (5)

> 
> 
> ## PR13540
> 
> x <- runif(200)
> b0 <- c(rep(0,100),runif(100))
> b1 <- 1
> fac <- as.factor(rep(c(0,1), each = 100))
> y <- b0 + b1*x + rnorm(200, sd=0.05)
> # next failed in 2.8.1
> fit <- nls(y~b0[fac] + b1*x, start = list(b0=c(1,1), b1=1),
+            algorithm ="port", upper = c(100, 100, 100))
> # next did not "fail" in proposed fix:
> fiB <- nls(y~b0[fac] + b1*x, start = list(b0=c(1,1), b1=101),
+            algorithm ="port", upper = c(100, 100, 100),
+            control = list(warnOnly=TRUE))# warning ..
Warning in nls(y ~ b0[fac] + b1 * x, start = list(b0 = c(1, 1), b1 = 101),  :
  Convergence failure: initial par violates constraints
> with(fiB$convInfo, ## start par. violates constraints
+      stopifnot(isConv == FALSE, stopCode == 300))
> 
> 
> ## PR#17367 -- nls() quoting non-syntactical variable names
> ##
> op <- options(warn = 2)# no warnings allowed from here
> ##
> dN <- data.frame('NO [µmol/l]' = c(1,3,8,17), t = 1:4, check.names=FALSE)
> fnN <- `NO [µmol/l]` ~ a + k* exp(t)
> ## lm() works,  nls() should too
> lm.N  <- lm(`NO [µmol/l]` ~ exp(t) ,                          data = dN)
> summary(lm.N) -> slmN
> nm. <- nls(`NO [µmol/l]` ~ a + k*exp(t), start=list(a=0,k=1), data = dN)
> ## In R <= 3.4.x : Error in eval(predvars, data, env) : object 'NO' not found
> nmf <- nls(fnN,                          start=list(a=0,k=1), data = dN)
> ## (ditto; gave identical error)
> noC  <- function(L) L[-match("call", names(L))]
> stopifnot(all.equal(noC (nm.), noC (nmf)))
> ##
> ## with list for which  as.data.frame() does not work [-> different branch, not using model.frame!]
> ## list version (has been valid "forever", still doubtful, rather give error [FIXME] ?)
> lsN <- c(as.list(dN), list(foo="bar")); lsN[["t"]] <- 1:8
> nmL <- nls(`NO [µmol/l]` ~ a + k*exp(t), start=list(a=0,k=1), data = lsN)
> stopifnot(all.equal(coef(nmL), c(a = 5.069866, k = 0.003699669), tol = 4e-7))# seen 4.2e-8
> 
> ## trivial RHS -- should work even w/o 'start='
> fi1 <- nls(y ~ a, start = list(a=1))
> ## -> 2 deprecation warnings "length 1 in vector-arithmetic" from nlsModel()  in R 3.4.x ..
> options(op) # warnings about missing 'start' ok:
> f.1 <- nls(y ~ a) # failed in R 3.4.x
Warning in nls(y ~ a) :
  No starting values specified for some parameters.
Initializing 'a' to '1.'.
Consider specifying 'start' or using a selfStart model
> stopifnot(all.equal(noC(f.1), noC(fi1)),
+ 	  all.equal(coef(f.1), c(a = mean(y))))
> 
> proc.time()
   user  system elapsed 
  1.610   0.053   1.661 
