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Paul Bernal

2023-Aug-20 19:16 UTC

[R] Issues when trying to fit a nonlinear regression model

Dear Bert,

Thank you for your extremely valuable feedback. Now, I just want to
understand why the signs for those starting values, given the
following:> #Fiting intermediate model to get starting values
> intermediatemod <- lm(log(y - .37) ~ x, data=mod14data2_random)
> summary(intermediatemod)
Call:
lm(formula = log(y - 0.37) ~ x, data = mod14data2_random)

Residuals:
    Min      1Q  Median      3Q     Max
-0.7946 -0.0908  0.0379  0.1111  0.5917

Coefficients:
            Estimate Std. Error t value Pr(>|t|)
(Intercept) -1.81693    0.25806   -7.04  8.8e-06 ***
x           -0.05538    0.00964   -5.75  6.8e-05 ***
---
Signif. codes:  0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1

Residual standard error: 0.323 on 13 degrees of freedom
Multiple R-squared:  0.717, Adjusted R-squared:  0.696
F-statistic:   33 on 1 and 13 DF,  p-value: 6.76e-05

Kind regards,
Paul

El dom, 20 ago 2023 a las 14:07, Bert Gunter (<bgunter.4567 at gmail.com>)
escribi?:
> Oh, sorry; I changed signs in the model, fitting
> theta0 + theta1*exp(theta2*x)
>
> So for theta0 - theta1*exp(-theta2*x) use theta1= -.exp(-1.8) and theta2
> +.055 as starting values.
>
> -- Bert
>
>
>
>
>
> On Sun, Aug 20, 2023 at 11:50?AM Paul Bernal <paulbernal07 at
gmail.com>
> wrote:
>
>> Dear Bert,
>>
>> Thank you so much for your kind and valuable feedback. I tried finding
>> the starting values using the approach you mentioned, then did the
>> following to fit the nonlinear regression model:
>> nlregmod2 <- nls(y ~ theta1 - theta2*exp(-theta3*x),
>>                   start >>                     list(theta1 =
0.37,
>>                          theta2 = exp(-1.8),
>>                          theta3 = -0.05538), data=mod14data2_random)
>> However, I got this error:
>> Error in nls(y ~ theta1 - theta2 * exp(-theta3 * x), start =
list(theta1
>> = 0.37,  :
>>   step factor 0.000488281 reduced below 'minFactor' of
0.000976562
>> nlregmod2 <- nlxb(y ~ theta1 - theta2*exp(-theta3*x),
>>                   start >>                     list(theta1 =
0.37,
>>                          theta2 = exp(-1.8),
>>                          theta3 = -0.05538), data=mod14data2_random)
>> summary(nlregmod2)
>> Object has try-error or missing parameters
>> nlregmod2
>> And I get some NA values when retrieving the statistics for the fitted
>> model:
>> residual sumsquares =  0.0022973  on  15 observations
>>     after  2235    Jacobian and  2861 function evaluations
>>   name            coeff          SE       tstat      pval      gradient
>>  JSingval
>> theta1           9330.89            NA         NA         NA  
5.275e-11
>>      967470
>> theta2           9330.41            NA         NA         NA 
-5.318e-11
>>       1.772
>> theta3       -3.0032e-07            NA         NA         NA  
1.389e-05
>>   8.028e-12
>>
>> Kind regards,
>> Paul
>>
>>
>> El dom, 20 ago 2023 a las 13:21, Bert Gunter (<bgunter.4567 at
gmail.com>)
>> escribi?:
>>
>>> I got starting values as follows:
>>> Noting that the minimum data value is .38, I fit the linear model
log(y
>>> - .37) ~ x to get intercept = -1.8 and slope = -.055. So I used
.37,
>>> exp(-1.8)  and -.055 as the starting values for theta0, theta1, and
theta2
>>> in the nonlinear model. This converged without problems.
>>>
>>> Cheers,
>>> Bert
>>>
>>>
>>> On Sun, Aug 20, 2023 at 10:15?AM Paul Bernal <paulbernal07 at
gmail.com>
>>> wrote:
>>>
>>>> Dear friends,
>>>>
>>>> This is the dataset I am currently working with:
>>>> >dput(mod14data2_random)
>>>> structure(list(index = c(14L, 27L, 37L, 33L, 34L, 16L, 7L, 1L,
>>>> 39L, 36L, 40L, 19L, 28L, 38L, 32L), y = c(0.44, 0.4, 0.4, 0.4,
>>>> 0.4, 0.43, 0.46, 0.49, 0.41, 0.41, 0.38, 0.42, 0.41, 0.4, 0.4
>>>> ), x = c(16, 24, 32, 30, 30, 16, 12, 8, 36, 32, 36, 20, 26, 34,
>>>> 28)), row.names = c(NA, -15L), class = "data.frame")
>>>>
>>>> I did the following to try to fit a nonlinear regression model:
>>>>
>>>> #First, Procedure to Find Starting (initial) Values For Theta1,
Theta2,
>>>> and
>>>> Theta3
>>>>
>>>> mymod2 <- y ~ theta1 - theta2*exp(-theta3*x)
>>>>
>>>> strt2 <- c(theta1 = 1, theta2 = 2, theta3 = 3)
>>>>
>>>> trysol2<-nlxb(formula=mymod2, data=mod14data2_random,
start=strt2,
>>>> trace=TRUE)
>>>> trysol2
>>>> trysol2$coefficients[[3]]
>>>>
>>>> #Fitting nonlinear Regression Model Using Starting Values From
Previous
>>>> Part
>>>> nonlinearmod2 <- nls(mymod2, start = list(theta1
>>>> trysol2$coefficients[[1]],
>>>>                      theta2 = trysol2$coefficients[[2]],
>>>>                      theta3 = trysol2$coefficients[[3]]), data
>>>> mod14data2_random)
>>>>
>>>> And I got this error:
>>>> Error in nlsModel(formula, mf, start, wts, scaleOffset = scOff,
>>>> nDcentral >>>> nDcntr) :
>>>>   singular gradient matrix at initial parameter estimates
>>>>
>>>> Any idea on how to proceed in this situation? What could I do?
>>>>
>>>> Kind regards,
>>>> Paul
>>>>
>>>>         [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> 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.
>>>>
>>>
	[[alternative HTML version deleted]]

Bert Gunter

2023-Aug-20 19:39 UTC

head link

[R] Issues when trying to fit a nonlinear regression model

Basic algebra and exponentials/logs. I leave those details to you or
another HelpeR.

-- Bert

On Sun, Aug 20, 2023 at 12:17?PM Paul Bernal <paulbernal07 at gmail.com>
wrote:
> Dear Bert,
>
> Thank you for your extremely valuable feedback. Now, I just want to
> understand why the signs for those starting values, given the following:
> > #Fiting intermediate model to get starting values
> > intermediatemod <- lm(log(y - .37) ~ x, data=mod14data2_random)
> > summary(intermediatemod)
>
> Call:
> lm(formula = log(y - 0.37) ~ x, data = mod14data2_random)
>
> Residuals:
>     Min      1Q  Median      3Q     Max
> -0.7946 -0.0908  0.0379  0.1111  0.5917
>
> Coefficients:
>             Estimate Std. Error t value Pr(>|t|)
> (Intercept) -1.81693    0.25806   -7.04  8.8e-06 ***
> x           -0.05538    0.00964   -5.75  6.8e-05 ***
> ---
> Signif. codes:  0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1
>
> Residual standard error: 0.323 on 13 degrees of freedom
> Multiple R-squared:  0.717, Adjusted R-squared:  0.696
> F-statistic:   33 on 1 and 13 DF,  p-value: 6.76e-05
>
> Kind regards,
> Paul
>
> El dom, 20 ago 2023 a las 14:07, Bert Gunter (<bgunter.4567 at
gmail.com>)
> escribi?:
>
>> Oh, sorry; I changed signs in the model, fitting
>> theta0 + theta1*exp(theta2*x)
>>
>> So for theta0 - theta1*exp(-theta2*x) use theta1= -.exp(-1.8) and
theta2
>> = +.055 as starting values.
>>
>> -- Bert
>>
>>
>>
>>
>>
>> On Sun, Aug 20, 2023 at 11:50?AM Paul Bernal <paulbernal07 at
gmail.com>
>> wrote:
>>
>>> Dear Bert,
>>>
>>> Thank you so much for your kind and valuable feedback. I tried
finding
>>> the starting values using the approach you mentioned, then did the
>>> following to fit the nonlinear regression model:
>>> nlregmod2 <- nls(y ~ theta1 - theta2*exp(-theta3*x),
>>>                   start >>>                    
list(theta1 = 0.37,
>>>                          theta2 = exp(-1.8),
>>>                          theta3 = -0.05538),
data=mod14data2_random)
>>> However, I got this error:
>>> Error in nls(y ~ theta1 - theta2 * exp(-theta3 * x), start =
list(theta1
>>> = 0.37,  :
>>>   step factor 0.000488281 reduced below 'minFactor' of
0.000976562
>>> nlregmod2 <- nlxb(y ~ theta1 - theta2*exp(-theta3*x),
>>>                   start >>>                    
list(theta1 = 0.37,
>>>                          theta2 = exp(-1.8),
>>>                          theta3 = -0.05538),
data=mod14data2_random)
>>> summary(nlregmod2)
>>> Object has try-error or missing parameters
>>> nlregmod2
>>> And I get some NA values when retrieving the statistics for the
fitted
>>> model:
>>> residual sumsquares =  0.0022973  on  15 observations
>>>     after  2235    Jacobian and  2861 function evaluations
>>>   name            coeff          SE       tstat      pval     
gradient
>>>    JSingval
>>> theta1           9330.89            NA         NA         NA  
5.275e-11
>>>      967470
>>> theta2           9330.41            NA         NA         NA 
-5.318e-11
>>>       1.772
>>> theta3       -3.0032e-07            NA         NA         NA  
1.389e-05
>>>   8.028e-12
>>>
>>> Kind regards,
>>> Paul
>>>
>>>
>>> El dom, 20 ago 2023 a las 13:21, Bert Gunter (<bgunter.4567 at
gmail.com>)
>>> escribi?:
>>>
>>>> I got starting values as follows:
>>>> Noting that the minimum data value is .38, I fit the linear
model log(y
>>>> - .37) ~ x to get intercept = -1.8 and slope = -.055. So I used
.37,
>>>> exp(-1.8)  and -.055 as the starting values for theta0, theta1,
and theta2
>>>> in the nonlinear model. This converged without problems.
>>>>
>>>> Cheers,
>>>> Bert
>>>>
>>>>
>>>> On Sun, Aug 20, 2023 at 10:15?AM Paul Bernal <paulbernal07
at gmail.com>
>>>> wrote:
>>>>
>>>>> Dear friends,
>>>>>
>>>>> This is the dataset I am currently working with:
>>>>> >dput(mod14data2_random)
>>>>> structure(list(index = c(14L, 27L, 37L, 33L, 34L, 16L, 7L,
1L,
>>>>> 39L, 36L, 40L, 19L, 28L, 38L, 32L), y = c(0.44, 0.4, 0.4,
0.4,
>>>>> 0.4, 0.43, 0.46, 0.49, 0.41, 0.41, 0.38, 0.42, 0.41, 0.4,
0.4
>>>>> ), x = c(16, 24, 32, 30, 30, 16, 12, 8, 36, 32, 36, 20, 26,
34,
>>>>> 28)), row.names = c(NA, -15L), class =
"data.frame")
>>>>>
>>>>> I did the following to try to fit a nonlinear regression
model:
>>>>>
>>>>> #First, Procedure to Find Starting (initial) Values For
Theta1,
>>>>> Theta2, and
>>>>> Theta3
>>>>>
>>>>> mymod2 <- y ~ theta1 - theta2*exp(-theta3*x)
>>>>>
>>>>> strt2 <- c(theta1 = 1, theta2 = 2, theta3 = 3)
>>>>>
>>>>> trysol2<-nlxb(formula=mymod2, data=mod14data2_random,
start=strt2,
>>>>> trace=TRUE)
>>>>> trysol2
>>>>> trysol2$coefficients[[3]]
>>>>>
>>>>> #Fitting nonlinear Regression Model Using Starting Values
From
>>>>> Previous Part
>>>>> nonlinearmod2 <- nls(mymod2, start = list(theta1
>>>>> trysol2$coefficients[[1]],
>>>>>                      theta2 = trysol2$coefficients[[2]],
>>>>>                      theta3 = trysol2$coefficients[[3]]),
data >>>>> mod14data2_random)
>>>>>
>>>>> And I got this error:
>>>>> Error in nlsModel(formula, mf, start, wts, scaleOffset =
scOff,
>>>>> nDcentral >>>>> nDcntr) :
>>>>>   singular gradient matrix at initial parameter estimates
>>>>>
>>>>> Any idea on how to proceed in this situation? What could I
do?
>>>>>
>>>>> Kind regards,
>>>>> Paul
>>>>>
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>> ______________________________________________
>>>>> 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.
>>>>>
>>>>
	[[alternative HTML version deleted]]

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