[R] How to coerce a parameter in nls?
Jianling Fan
fanjianling at gmail.com
Mon Sep 21 19:03:11 CEST 2015
Thanks Gabor,
That works good to rewrite the express the formula!
Thanks a lot!
Regards,
Jianling
On 21 September 2015 at 10:43, Gabor Grothendieck
<ggrothendieck at 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 <fanjianling at 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 <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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