Another alternative is to use SSlogis which is very similar to the
model you're fitting except with one additional parameter:
Asym <- 3
xmid <- 0
scal <- 10
model <- nls(bod ~ SSlogis(time, Asym, xmid, scal), data = mydata)
summary(model)
plot(bod ~ time, mydata)
newdata <- data.frame(time = seq(1, 11, length = 100))
lines(newdata$time, predict(model, newdata))
HTH,
--sundar
On Tue, Aug 25, 2009 at 10:05 AM, Sundar Dorai-Raj<sdorai...@gmail.com> wrote:
> Hi, Michael,
>
> I think the SPSS answer is wrong. Your starting values are way off.
> Look at this plot for verification:
>
> con <- textConnection("time bod
> 1 1 0.47
> 2 2 0.74
> 3 3 1.17
> 4 4 1.42
> 5 5 1.60
> 6 7 1.84
> 7 9 2.19
> 8 11 2.17")
> mydata <- read.table(con, header = TRUE)
> close(con)
>
> beta <- c(3, -0.1) # your initial values
> beta <- c(2.4979, -2.02456) # SPSS answer
> mycurve <- function(x) {
> beta[1]/(1 - exp(beta[1] * x))
> }
> curve(mycurve, from = 1, to = 11,
> ylim = range(mydata$bod, mycurve(mydata$time)))
> points(mydata$time, mydata$bod)
>
> You might want to look at package nls2 which allows a brute force grid
> search to find some starting values. Or rethink the equation you're
> trying to fit.
>
> HTH,
>
> --sundar
>
> On Tue, Aug 25, 2009 at 9:10 AM, Michael Pearmain<mpearm...@google.com> wrote:
>> Hi All,
>>
>> I'm trying to run nls on the data from the study by Marske (Biochemical
>> Oxygen Demand Interpretation Using Sum of Squares Surface. M.S. thesis,
>> University of Wisconsin, Madison, 1967) and was reported in Bates and Watts
>> (1988).
>>
>> Data is as follows, (stored as mydata)
>>
>> time bod
>> 1 1 0.47
>> 2 2 0.74
>> 3 3 1.17
>> 4 4 1.42
>> 5 5 1.60
>> 6 7 1.84
>> 7 9 2.19
>> 8 11 2.17
>>
>> I then run the following;
>> #Plot initial curve
>> plot(mydata$time, mydata$bod,xlab="Time (in days)",ylab="biochemical oxygen
>> demand (mg/l) ")
>>
>> model <- nls(bod ~ beta1/(1 - exp(beta2*time)), data =
>> mydata, start=list(beta1 = 3, beta2 = -0.1),trace=T)
>>
>> The start values are recommended, (I have used these values in SPSS without
>> any problems, SPSS returns values of Beta1 = 2.4979 and Beta2 = -2.02 456)
>>
>> but return the error message,
>> Error in nls(bod ~ beta1/(1 - exp(beta2 * time)), data = mydata, start =
>> list(beta1 = 3, : singular gradient
>>
>> Can anyone offer any advice?
>>
>> Thanks in advance
>>
>> Mike
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> Michael Pearmain
>> Senior Analytics Research Specialist
>>
>> “Statistics are like women; mirrors of purest virtue and truth, or like
>> whores to use as one pleases”
>>
>> Google UK Ltd
>> Belgrave House
>> 76 Buckingham Palace Road
>> London SW1W 9TQ
>> United Kingdom
>> t +44 (0) 2032191684
>> mpearm...@google.com
>>
>> If you received this communication by mistake, please don't forward it to
>> anyone else (it may contain confidential or privileged information), please
>> erase all copies of it, including all attachments, and please let the sender
>> know it went to the wrong person. Thanks.
>>
>> [[alternative HTML version deleted]]
>>
>>
>> ______________________________________________
>> R-help@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
______________________________________________
R-help@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
