You may have to do without masking and switch back to nls. dproot2 and fo are from prior post.
# to mask Rm6 omit it from start and set it explicitly st <- c(Rm1=1.01, Rm2=1.01, Rm3=1.01, Rm4=6.65, Rm5=1.01, d50=20, c=-1) Rm6 <- 1 fm.nls <- nls(fo, dproot2, start = st) AIC(fm.nls) summary(fm.nls) On Tue, Sep 22, 2015 at 12:46 PM, Jianling Fan <fanjianl...@gmail.com> wrote: > Hello Prof. Nash, > > My regression works good now. But I found another problem when I using > nlxb. In the output, the SE, t-stat, and p-value are not available. > Furthermore, I can't extract AIC from the output. The output looks > like below: > > Do you have any suggestion for this? > > Thanks a lot! > > Regards, > > nlmrt class object: x > residual sumsquares = 0.29371 on 33 observations > after 9 Jacobian and 10 function evaluations > name coeff SE tstat pval > gradient JSingval > Rm1 1.1162 NA NA NA > -3.059e-13 2.745 > Rm2 1.56072 NA NA NA > 1.417e-13 1.76 > Rm3 1.09775 NA NA NA > -3.179e-13 1.748 > Rm4 7.18377 NA NA NA > -2.941e-12 1.748 > Rm5 1.13562 NA NA NA > -3.305e-13 1.076 > Rm6 1 M NA NA NA > 0 0.603 > d50 22.4803 NA NA NA > 4.975e-13 0.117 > c -1.64075 NA NA NA > 4.12e-12 1.908e-17 > > > > On 21 September 2015 at 13:38, ProfJCNash <profjcn...@gmail.com> wrote: > > I've not used it for group data, and suspect that the code to generate > > derivatives cannot cope with the bracket syntax. If you can rewrite the > > equation without the brackets, you could get the derivatives and solve > that > > way. This will probably mean having a "translation" routine to glue > things > > together. > > > > JN > > > > > > On 15-09-21 12:22 PM, Jianling Fan 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 [[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.