Hello, Gabor, Thanks again for your suggestion. And now I am trying to improve the code by adding a function to replace the express "Rm1 * ref.1 + Rm2 * ref.2 + Rm3 * ref.3 + Rm4 * ref.4 + Rm5 * ref.5 + Rm6 * ref.6" because I have some other dataset need to fitted to the same model but with more groups (>20).
I tried to add the function as: denfun<-function(i){ for(i in 1:6){ Rm<-sum(Rm[i]*ref.i) return(Rm)} } but I got another error when I incorporate this function into my regression: >fitdp1<-nlxb(den ~ denfun(6)/(1+(depth/d50)^c), data = dproot2, start = c(Rm1=1.01, Rm2=1.01, Rm3=1.01, Rm4=6.65, Rm5=1.01, Rm6=1, d50=20, c=-1), masked = "Rm6") Error in deriv.default(parse(text = resexp), names(start)) : Function 'denfun' is not in the derivatives table I think there must be something wrong with my function. I tried some times but am not sure how to improve it because I am quite new to R. Could anyone please give me some suggestion. Thanks a lot! Jianling On 22 September 2015 at 00:43, Gabor Grothendieck <ggrothendi...@gmail.com> wrote: > Express the formula in terms of simple operations like this: > > # add 0/1 columns ref.1, ref.2, ..., ref.6 > dproot2 <- do.call(data.frame, transform(dproot, ref = outer(dproot$ref, > seq(6), "==") + 0)) > > # now express the formula in terms of the new columns > library(nlmrt) > fitdp1<-nlxb(den ~ (Rm1 * ref.1 + Rm2 * ref.2 + Rm3 * ref.3 + Rm4 * ref.4 + > Rm5 * ref.5 + Rm6 * ref.6)/(1+(depth/d50)^c), > data = dproot2, > start = c(Rm1=1.01, Rm2=1.01, Rm3=1.01, Rm4=6.65, Rm5=1.01, Rm6=1, > d50=20, c=-1), > masked = "Rm6") > > where we used this input: > > Lines <- " depth den ref > 1 20 0.5730000 1 > 2 40 0.7800000 1 > 3 60 0.9470000 1 > 4 80 0.9900000 1 > 5 100 1.0000000 1 > 6 10 0.6000000 2 > 7 20 0.8200000 2 > 8 30 0.9300000 2 > 9 40 1.0000000 2 > 10 20 0.4800000 3 > 11 40 0.7340000 3 > 12 60 0.9610000 3 > 13 80 0.9980000 3 > 14 100 1.0000000 3 > 15 20 3.2083491 4 > 16 40 4.9683383 4 > 17 60 6.2381133 4 > 18 80 6.5322348 4 > 19 100 6.5780660 4 > 20 120 6.6032064 4 > 21 20 0.6140000 5 > 22 40 0.8270000 5 > 23 60 0.9500000 5 > 24 80 0.9950000 5 > 25 100 1.0000000 5 > 26 20 0.4345774 6 > 27 40 0.6654726 6 > 28 60 0.8480684 6 > 29 80 0.9268951 6 > 30 100 0.9723207 6 > 31 120 0.9939966 6 > 32 140 0.9992400 6" > > dproot <- read.table(text = Lines, header = TRUE) > > > > On Mon, Sep 21, 2015 at 12:22 PM, Jianling Fan <fanjianl...@gmail.com> > wrote: >> >> Thanks Prof. Nash, >> >> Sorry for late reply. I am learning and trying to use your nlmrt >> package since I got your email. It works good to mask a parameter in >> regression but seems does work for my equation. I think the problem is >> that the parameter I want to mask is a group-specific parameter and I >> have a "[]" syntax in my equation. However, I don't have your 2014 >> book on hand and couldn't find it in our library. So I am wondering if >> nlxb works for group data? >> Thanks a lot! >> >> following is my code and I got a error form it. >> >> > fitdp1<-nlxb(den~Rm[ref]/(1+(depth/d50)^c),data=dproot, >> + start =c(Rm1=1.01, Rm2=1.01, Rm3=1.01, Rm4=6.65, >> Rm5=1.01, Rm6=1, d50=20, c=-1), >> + masked=c("Rm6")) >> >> Error in deriv.default(parse(text = resexp), names(start)) : >> Function '`[`' is not in the derivatives table >> >> >> Best regards, >> >> Jianling >> >> >> On 20 September 2015 at 12:56, ProfJCNash <profjcn...@gmail.com> wrote: >> > I posted a suggestion to use nlmrt package (function nlxb to be >> > precise), >> > which has masked (fixed) parameters. Examples in my 2014 book on >> > Nonlinear >> > parameter optimization with R tools. However, I'm travelling just now, >> > or >> > would consider giving this a try. >> > >> > JN >> > >> > >> > On 15-09-20 01:19 PM, Jianling Fan wrote: >> >> >> >> no, I am doing a regression with 6 group data with 2 shared parameters >> >> and 1 different parameter for each group data. the parameter I want to >> >> coerce is for one group. I don't know how to do it. Any suggestion? >> >> >> >> Thanks! >> >> >> >> On 19 September 2015 at 13:33, Jeff Newmiller >> >> <jdnew...@dcn.davis.ca.us> >> >> wrote: >> >>> >> >>> Why not rewrite the function so that value is not a parameter? >> >>> >> >>> >> >>> --------------------------------------------------------------------------- >> >>> Jeff Newmiller The ..... ..... Go >> >>> Live... >> >>> DCN:<jdnew...@dcn.davis.ca.us> Basics: ##.#. ##.#. Live >> >>> Go... >> >>> Live: OO#.. Dead: OO#.. >> >>> Playing >> >>> Research Engineer (Solar/Batteries O.O#. #.O#. with >> >>> /Software/Embedded Controllers) .OO#. .OO#. >> >>> rocks...1k >> >>> >> >>> >> >>> --------------------------------------------------------------------------- >> >>> Sent from my phone. Please excuse my brevity. >> >>> >> >>> On September 18, 2015 9:54:54 PM PDT, Jianling Fan >> >>> <fanjianl...@gmail.com> wrote: >> >>>> >> >>>> Hello, everyone, >> >>>> >> >>>> I am using a nls regression with 6 groups data. I am trying to coerce >> >>>> a parameter to 1 by using a upper and lower statement. but I always >> >>>> get an error like below: >> >>>> >> >>>> Error in ifelse(internalPars < upper, 1, -1) : >> >>>> (list) object cannot be coerced to type 'double' >> >>>> >> >>>> does anyone know how to fix it? >> >>>> >> >>>> thanks in advance! >> >>>> >> >>>> My code is below: >> >>>> >> >>>> >> >>>> >> >>>>> dproot >> >>>> >> >>>> depth den ref >> >>>> 1 20 0.5730000 1 >> >>>> 2 40 0.7800000 1 >> >>>> 3 60 0.9470000 1 >> >>>> 4 80 0.9900000 1 >> >>>> 5 100 1.0000000 1 >> >>>> 6 10 0.6000000 2 >> >>>> 7 20 0.8200000 2 >> >>>> 8 30 0.9300000 2 >> >>>> 9 40 1.0000000 2 >> >>>> 10 20 0.4800000 3 >> >>>> 11 40 0.7340000 3 >> >>>> 12 60 0.9610000 3 >> >>>> 13 80 0.9980000 3 >> >>>> 14 100 1.0000000 3 >> >>>> 15 20 3.2083491 4 >> >>>> 16 40 4.9683383 4 >> >>>> 17 60 6.2381133 4 >> >>>> 18 80 6.5322348 4 >> >>>> 19 100 6.5780660 4 >> >>>> 20 120 6.6032064 4 >> >>>> 21 20 0.6140000 5 >> >>>> 22 40 0.8270000 5 >> >>>> 23 60 0.9500000 5 >> >>>> 24 80 0.9950000 5 >> >>>> 25 100 1.0000000 5 >> >>>> 26 20 0.4345774 6 >> >>>> 27 40 0.6654726 6 >> >>>> 28 60 0.8480684 6 >> >>>> 29 80 0.9268951 6 >> >>>> 30 100 0.9723207 6 >> >>>> 31 120 0.9939966 6 >> >>>> 32 140 0.9992400 6 >> >>>> >> >>>>> fitdp<-nls(den~Rm[ref]/(1+(depth/d50)^c),data=dproot, >> >>>> >> >>>> + start = list(Rm=c(1.01, 1.01, 1.01, 6.65,1.01,1), d50=20, c=-1)) >> >>>>> >> >>>>> summary(fitdp) >> >>>> >> >>>> >> >>>> Formula: den ~ Rm[ref]/(1 + (depth/d50)^c) >> >>>> >> >>>> Parameters: >> >>>> Estimate Std. Error t value Pr(>|t|) >> >>>> Rm1 1.12560 0.07156 15.73 3.84e-14 *** >> >>>> Rm2 1.57643 0.11722 13.45 1.14e-12 *** >> >>>> Rm3 1.10697 0.07130 15.53 5.11e-14 *** >> >>>> Rm4 7.23925 0.20788 34.83 < 2e-16 *** >> >>>> Rm5 1.14516 0.07184 15.94 2.87e-14 *** >> >>>> Rm6 1.03658 0.05664 18.30 1.33e-15 *** >> >>>> d50 22.69426 1.03855 21.85 < 2e-16 *** >> >>>> c -1.59796 0.15589 -10.25 3.02e-10 *** >> >>>> --- >> >>>> Signif. codes: 0 ?**?0.001 ?*?0.01 ??0.05 ??0.1 ??1 >> >>>> >> >>>> Residual standard error: 0.1094 on 24 degrees of freedom >> >>>> >> >>>> Number of iterations to convergence: 8 >> >>>> Achieved convergence tolerance: 9.374e-06 >> >>>> >> >>>>> fitdp1<-nls(den~Rm[ref]/(1+(depth/d50)^c),data=dproot, >> >>>> >> >>>> algorithm="port", >> >>>> + start = list(Rm=c(1.01, 1.01, 1.01, 6.65, 1.01, 1), d50=20, c=-1), >> >>>> + lower = list(Rm=c(1.01, 1.01, 1.01, 6.65, 1.01, 1), d50=20, c=-1), >> >>>> + upper = list(Rm=c(2.1, 2.2, 2.12, 12.5, 2.3, 1), d50=50, c=1)) >> >>>> >> >>>> Error in ifelse(internalPars < upper, 1, -1) : >> >>>> (list) object cannot be coerced to type 'double' >> >>>> >> >>>> ______________________________________________ >> >>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> >>>> 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 -- To UNSUBSCRIBE and more, see >> > 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. >> >> >> >> -- >> Jianling Fan >> 樊建凌 >> >> ______________________________________________ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> 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. > > > > > -- > Statistics & Software Consulting > GKX Group, GKX Associates Inc. > tel: 1-877-GKX-GROUP > email: ggrothendieck at gmail.com -- Jianling Fan 樊建凌 ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.