[R] How to coerce a parameter in nls?

ProfJCNash profjcnash at gmail.com
Mon Sep 21 21:38:48 CEST 2015


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
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>>>>> PLEASE do read the posting guide
>>>>> http://www.R-project.org/posting-guide.html
>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>>
>>>>
>>>
>>>
>>>
>>
>> ______________________________________________
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>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>
>



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