# [R] How to coerce a parameter in nls?

Gabor Grothendieck ggrothendieck at gmail.com
Mon Sep 21 18:43:42 CEST 2015

```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),

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"

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),
>
> 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?
> >>>>
> >>>>
> >>>> 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
> >>>> 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
> 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
> 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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