R help - Jun 2020 - invalid type (list) for variable 'y' in library minpack.lm

Hello,
I am trying to find the best fit to a function for epidemic analysis.
I am trying with the package minpack.lm but I don't really know how to
use it. I am getting the error:
```
Error in model.frame.default(formula = ~y + x, data = list(Y)) :
  invalid type (list) for variable 'y'
In addition: Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf
```
So I have some questions:
- how to solve the list problem? (what is the input for nlsLM? I have
a vector with the actual values, shall I convert in a dataframe?)
- how to avoid infinitives?
- is there another function other than nlsLM that I should use?
- is there another function that could fit a sigmoid profile other
than Holling type III?

This is the working example:
```
holling = function(a, b, x) {
  y = (a * x^2) / (b^2 + x^2)
  return(y)
}
Y = c(8,   24,   39,   63,   89,  115,  153,  196,  242,  287,  344,  408,  473,
      546,  619,  705,  794,  891,  999, 1096, 1242, 1363, 1506, 1648, 1753,
      1851, 1987, 2101, 2219, 2328, 2425, 2575, 2646, 2698, 2727, 2771, 2818,
      2853, 2895, 2926, 2964, 2995, 3025, 3053, 3080, 3102, 3119, 3141, 3152,
      3159, 3172, 3182, 3196, 3209, 3220, 3231, 3239, 3246, 3252, 3261)
X = 1:60
A = 3261
B = 10
plot(X, Y,
     col = "red", pch =16, lwd = 2,
     main = paste("Starting values: a=", A, "; b=", B, sep
=""),
     xlab = expression(bold("Days of infection")),
     ylab = expression(bold("Cumulative incidence")))
HL = holling(A, B, X)
points(X, HL, type = "l", lty = 2)

# estimation
library("minpack.lm")
init_parms = c(a=A, b=B)
est = nlsLM(formula = y~(a*x^2)/(b^2 + x^2), start=init_parms, data=list(Y))
```

-- 
Best regards,
Luigi

Dear Luigi,

On 2020-06-25 12:18 +0200, Luigi Marongiu wrote:
> Hello,
> I am trying to find the best fit to a 
> function for epidemic analysis.
> I am trying with the package minpack.lm but 
> I don't really know how to use it.
Me neither ...
> So I have some questions:
> - how to solve the list problem? (what is 
>   the input for nlsLM? I have a vector with 
>   the actual values, shall I convert in a 
>   dataframe?)
I got past the error by give 
minpack.lm::nlsLM X and Y in a data.frame

	minpack.lm::nlsLM(
	  formula = y~(a*x^2)/(b^2 + x^2),
	  start=c(a=A, b=B),
	  data=data.frame(x=X, y=Y))

as per ?minpack.lm::nlsLM:

	data: an optional data frame in which to evaluate the variables
	      in?formula? and ?weights?.  Can also be a list or an
	      environment, but not a matrix.
> - how to avoid infinitives?
> - is there another function other than 
>   nlsLM that I should use?
> - is there another function that could fit 
>   a sigmoid profile other than Holling type 
>   III?
These other questions seem good and 
interesting, I hope someone else can answer 
them.

Best,
Rasmus

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"These other questions seem good and
interesting, I hope someone else can answer
them."

Perhaps, but not appropriate for this list, imo. Statistics issue mostly
belong elsewhere, e.g. on stats.stackexchange.com.

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Thu, Jun 25, 2020 at 4:25 AM Rasmus Liland <jral at posteo.no> wrote:
> Dear Luigi,
>
> On 2020-06-25 12:18 +0200, Luigi Marongiu wrote:
> > Hello,
> > I am trying to find the best fit to a
> > function for epidemic analysis.
> > I am trying with the package minpack.lm but
> > I don't really know how to use it.
>
> Me neither ...
>
> > So I have some questions:
> > - how to solve the list problem? (what is
> >   the input for nlsLM? I have a vector with
> >   the actual values, shall I convert in a
> >   dataframe?)
>
> I got past the error by give
> minpack.lm::nlsLM X and Y in a data.frame
>
>         minpack.lm::nlsLM(
>           formula = y~(a*x^2)/(b^2 + x^2),
>           start=c(a=A, b=B),
>           data=data.frame(x=X, y=Y))
>
> as per ?minpack.lm::nlsLM:
>
>         data: an optional data frame in which to evaluate the variables
>               in?formula? and ?weights?.  Can also be a list or an
>               environment, but not a matrix.
>
> > - how to avoid infinitives?
> > - is there another function other than
> >   nlsLM that I should use?
> > - is there another function that could fit
> >   a sigmoid profile other than Holling type
> >   III?
>
> These other questions seem good and
> interesting, I hope someone else can answer
> them.
>
> Best,
> Rasmus
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