Or if you really can't bear to write out 20 terms have R do it for you: # number of terms is the number of unique values in ref column nterms <- length(unique(dproot$ref))
dproot2 <- do.call(data.frame, transform(dproot, ref = outer(dproot$ref, seq(nterms), "==") + 0)) # construct the formula as a string terms <- paste( sprintf("Rm%d*ref.%d", 1:nterms, 1:nterms), collapse = "+") fo <- sprintf("den ~ (%s)/(1+(depth/d50)^c)", terms) library(nlmrt) fm <- nlxb(fo, data = dproot2, masked = "Rm6", start = c(Rm1=1.01, Rm2=1.01, Rm3=1.01, Rm4=6.65, Rm5=1.01, Rm6=1, d50=20, c=-1)) On Tue, Sep 22, 2015 at 7:04 AM, Gabor Grothendieck <ggrothendi...@gmail.com > wrote: > Just write out the 20 terms. > > On Mon, Sep 21, 2015 at 10:26 PM, Jianling Fan <fanjianl...@gmail.com> > wrote: > >> 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 >> > > > > -- > Statistics & Software Consulting > GKX Group, GKX Associates Inc. > tel: 1-877-GKX-GROUP > email: ggrothendieck at gmail.com > -- Statistics & Software Consulting GKX Group, GKX Associates Inc. tel: 1-877-GKX-GROUP email: ggrothendieck at gmail.com [[alternative HTML version deleted]] ______________________________________________ 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.