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:> dprootdepth 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'
Why not rewrite the function so that value is not a parameter?
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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.
You need to read the help more closely. start should be a list, as you've done, but upper and lower should be vectors instead. Which is exactly what your error message is telling you. lower, upper vectors of lower and upper bounds, replicated to be as long as start. If unspecified, all parameters are assumed to be unconstrained. Bounds can only be used with the "port" algorithm. They are ignored, with a warning, if given for other algorithms. Sarah On Saturday, September 19, 2015, 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 <javascript:;> 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. >-- Sarah Goslee http://www.stringpage.com http://www.sarahgoslee.com http://www.functionaldiversity.org [[alternative HTML version deleted]]
Besides this, using bounds to fix (also called "mask") parameters is generally a very bad idea. Some optimization methods allow this explicitly. For nonlinear least squares nlmrt package has it, but I'm not sure I fully documented the process. For optimization, Rvmmin and Rcgmin both allow masks, but again the documentation is not fully developed. There is a section in my 2014 book Nonlinear Parameter Optimization in R. I'm on vacation, and don't have the page refs. at this moment, however. I know there are some other packages that include the possibility of fixed parameters, and perhaps others could give pointers, as I don't have the references with me. JN On 15-09-19 05:10 AM, Sarah Goslee wrote:> You need to read the help more closely. start should be a list, as you've > done, but upper and lower should be vectors instead. Which is exactly what > your error message is telling you. > > lower, upper > > vectors of lower and upper bounds, replicated to be as long as start. If > unspecified, all parameters are assumed to be unconstrained. Bounds can > only be used with the "port" algorithm. They are ignored, with a warning, > if given for other algorithms. > Sarah > > On Saturday, September 19, 2015, 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 <javascript:;> 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. >> > >
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. >-- Jianling Fan ???