nonlinear regression with exp(-exp(-x/c)) as model (R,nls)

Question

I have a hard time fitting the following model to subsequent data:

y = a * exp( - b * exp( - x/c))

DF$x=c(200,300,400,500,600,700,800,900,1000,1100,1200,1300,1400,1500,1600,1700,1800,1900,2000,2100,2200,2300,2400,2500,2600,2700,2800,2900,3000,3100,3200,3300,3400,3500,3600,3700,3800,3900,4000,4100,4200,4300,4400,4500,4600,4700,4800,4900,5000,5100,5200,5300,5400,5500,5600,5700,5800,5900,6000,6100,6200,6300,6400,6500,6600,6700,6800,6900,7000)
DF$y=c(50,150,350,550,1050,1650,2950,4750,7850,12350,18950,27250,36750,49750,63250,79050,95450,112850,134550,158050,184650,211150,237750,270150,299650,334850,373450,413050,453050,490350,534250,574050,622750,666550,707350,760250,803050,848650,893850,928250,973850,1006250,1047650,1075850,1113850,1146350,1180150,1212650,1243950,1275850,1306250,1332150,1372350,1402550,1440650,1471550,1503550,1549850,1583150,1628850,1664250,1711250,1746850,1793250,1837950,1884750,1930850,1976750,2008650)

Actually, I need a log(y, base = 10) plot. So when I use ggplot and stat_smooth(method='nls',...), I end up with a horrible fit. And I do not know how to improve the fit. Can you think of a reasonable approach? Thanks !

My code so far :

ggplot(DF, aes(x = x, y = y)) + geom_point() + 
stat_smooth(method = 'nls', 
    formula = y ~ a * exp(- b * exp( - x / 50 )), 
    aes(colour = 'Exponential'), 
    se = FALSE,   start = list(a=1000,b=10)) +
    scale_y_continuous(trans='log10')

Your code is right. You need either better starting values or a better model. — Matthew Plourde, Dec 07 '15 at 14:14
True. I already got reasonable start values (cf. added code). But I need ways to improve the fit, though. I am rather new to R-fitting, so I need some in-depth approaches with this explicit example. The model is based on experimental data. The data shown here is from a simulation. — m2k1, Dec 07 '15 at 14:15
` y ~ SSasymp(x, Asym, R0, lrc)` works well with no starting values — Matthew Plourde, Dec 07 '15 at 14:17
Thanks, I'll look into this. The model I posted is essential, though. I cannot replace it. My data is very similar to the experimental data, so there should be a satisfactory fit. The fit to the experimental data has already been published by so else. — m2k1, Dec 07 '15 at 14:21
Can you clarify whether this is specifically a ggplot question, or whether getting `nls` to work as a stand-alone operation (and then possibly adding it to a ggplot call) would be sufficient? — Ben Bolker, Dec 07 '15 at 15:01
@BenBolker - thanks for your interest. Of course the main issue is `nls`. Plotting with the use of `ggplot` is of minor importance. — m2k1, Dec 07 '15 at 16:23
You say "I already got reasonable start values " `(a=1000,b=10)`, but I'm not convinced. Following you in fixing `c=50` I persuaded nls to converge to values of `(a=1.328e+06, b=7.270e+28)` — user20637, Dec 07 '15 at 17:21
@user20637 - meanwhile, after some playing around, I obtained these starting values: `a=1843000,b=18,c=12` . I have to add that I divided all DF$x values by a factor of 100 — m2k1, Dec 07 '15 at 18:02

score 2 · Accepted Answer · answered Dec 08 '15 at 17:16

tl;dr You are trying to fit a Gompertz curve, and R has an SSgompertz function that does the trick.

Data:

x <- seq(200,7000,by=100)
y <- c(50,150,350,550,1050,1650,2950,4750,7850,12350,18950,27250,36750,49750,63250,79050,95450,112850,134550,158050,184650,211150,237750,270150,299650,334850,373450,413050,453050,490350,534250,574050,622750,666550,707350,760250,803050,848650,893850,928250,973850,1006250,1047650,1075850,1113850,1146350,1180150,1212650,1243950,1275850,1306250,1332150,1372350,1402550,1440650,1471550,1503550,1549850,1583150,1628850,1664250,1711250,1746850,1793250,1837950,1884750,1930850,1976750,2008650)
DF <- data.frame(x,y)

The parameterization of R's self-starting Gompertz function (?SSgompertz) is a*exp(-b2*b3^x) = a*exp(-b2*exp(x*log(b3)) = a*exp(-b2*exp(x/(1/log(b3)))

library("ggplot2"); theme_set(theme_bw())
n1 <- nls(y ~ SSgompertz(x, p1,p2,p3 ), data=DF)
coef(n1)
##           p1           p2          p3
## 2.530746e+06 6.907014e+00 9.995405e-01

Translating this into your terms:

coef2 <- with(as.list(coef(n1)),
            c(a=p1,b=p2,c=-1/log(p3)))

##             a            b             c 
##  2.530746e+06 6.907014e+00  2.175813e+03

Check:

tmpf0 <- function(x) {
    with(as.list(coef(n1)),p1*exp(-p2*p3^x))
}

tmpf <- function(x) {
    y <- with(as.list(coef2),a*exp(-b*exp(-x/c)))
    print(range(y))
    return(y)
}
tmpf0(200)  ## 4645.226
tmpf(200)   ## ditto

I can easily draw the plot with the predicted values, but for reasons I can't currently figure out I can't (1) embed the fit within ggplot2 (2) use stat_function() with tmpf to add the results to the plot.

DF$pred <- predict(n1)
g0 <- ggplot(DF,aes(x,y))+geom_point()
g0+ geom_line(aes(y=pred),colour="red") +
        scale_y_log10()

nonlinear regression with exp(-exp(-x/c)) as model (R,nls)

1 Answers1