[R] How to coerce a parameter in nls?
Jianling Fan
fanjianling at gmail.com
Tue Sep 22 20:55:24 CEST 2015
great, Thanks a lot!
On 22 September 2015 at 12:07, Gabor Grothendieck
<ggrothendieck at gmail.com> wrote:
> 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 <fanjianling at 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 <profjcnash at 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 <profjcnash at 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
>> >>>> <jdnewmil at dcn.davis.ca.us>
>> >>>> wrote:
>> >>>>>
>> >>>>>
>> >>>>> Why not rewrite the function so that value is not a parameter?
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> ---------------------------------------------------------------------------
>> >>>>> Jeff Newmiller The ..... ..... Go
>> >>>>> Live...
>> >>>>> DCN:<jdnewmil at 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
>> >>>>> <fanjianling at 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 at 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 at 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 at 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
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