[R] How to coerce a parameter in nls?
ProfJCNash
profjcnash at gmail.com
Mon Sep 21 21:40:00 CEST 2015
Apologies for replying and overlapping Gabor's contribution, which
actually did the work!
Best, JN
On 15-09-21 01:03 PM, Jianling Fan wrote:
> 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
>
>
>
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