Marc:
1. I am aware of the need to explicitly name arguments after ... --
see the R Language definition where this can be inferred from the
argument matching rules.
2. I am aware of the stated exception for poly(). However:
> x1 <- runif(20)
> x2 <- runif(20)
> mx <- cbind(x1,x2)
> poly(mx,2)
Error in poly(dots[[i]], degree, raw = raw, simple = raw) :
'degree' must be less than number of unique points
> poly(mx, degree = 2)
1.0 2.0 0.1 1.1 0.2
[1,] -0.2984843 0.0402593349 -0.07095761 0.021179734 -0.22909595
[2,] 0.2512177 0.2172530896 0.29620999 0.074413206 0.14508422
[3,] 0.2775652 0.3085750335 -0.13955410 -0.038735366 -0.13729529
[4,] -0.4090782 0.4032189266 -0.14737858 0.060289370 -0.12358925
[5,] -0.1631886 -0.2221937915 -0.26690975 0.043556631 0.16814432
[6,] 0.1770952 0.0009863446 0.25380650 0.044947925 0.02737265
[7,] -0.2108146 -0.1525957018 0.34023304 -0.071726094 0.28787441
[8,] 0.2693983 0.2794576400 0.04697126 0.012653979 -0.26792015
[9,] 0.2014353 0.0653896008 -0.37013148 -0.074557536 0.54445808
[10,] -0.1002967 -0.2761638672 -0.29389518 0.029476714 0.25539539
[11,] 0.1132090 -0.1372916959 0.21619808 0.024475573 -0.06074932
[12,] -0.1116108 -0.2696398425 -0.14592886 0.016287234 -0.12617869
[13,] 0.1792535 0.0064357827 -0.04948750 -0.008870809 -0.24736773
[14,] -0.1167216 -0.2662346206 -0.20209364 0.023588696 -0.00923419
[15,] -0.4258838 0.4700591049 0.08836730 -0.037634205 -0.24586894
[16,] 0.1047271 -0.1523001267 -0.21491954 -0.022507896 0.02225837
[17,] -0.1985753 -0.1728455549 0.32036901 -0.063617358 0.22084868
[18,] 0.1844006 0.0196368680 0.32321195 0.059600465 0.23017961
[19,] 0.1009775 -0.1586846110 -0.08282554 -0.008363512 -0.21685556
[20,] 0.1753745 -0.0033219134 0.09871464 0.017312033 -0.23746062
attr(,"degree")
[1] 1 2 1 2 2
attr(,"coefs")
attr(,"coefs")[[1]]
attr(,"coefs")[[1]]$alpha
[1] 0.5477073 0.4154115
attr(,"coefs")[[1]]$norm2
[1] 1.00000000 20.00000000 1.55009761 0.08065872
Cheers,
Bert
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, Jul 13, 2017 at 11:17 AM, Marc Schwartz <marc_schwa...@me.com> wrote:
> Bert,
>
> The 'degree' argument follows the "..." argument in the function declaration:
>
> poly(x, ..., degree = 1, coefs = NULL, raw = FALSE, simple = FALSE)
>
> Generally, any arguments after the "..." must be explicitly named, but as per
> the Details section of ?poly:
>
> "Although formally degree should be named (as it follows ...), an unnamed
> second argument of length 1 will be interpreted as the degree, such that
> poly(x, 3) can be used in formulas."
>
> The issue of having to explicitly name arguments that follow the three dots
> has come up over the years, but I cannot recall where that is documented in
> the manuals.
>
> Regards,
>
> Marc
>
>
>
>> On Jul 13, 2017, at 12:43 PM, Bert Gunter <bgunter.4...@gmail.com> wrote:
>>
>> poly(NIR, degree = 2) will work if NIR is a matrix, not a data.frame.
>> The degree argument apparently *must* be explicitly named if NIR is
>> not a numeric vector. AFAICS, this is unclear or unstated in ?poly.
>>
>>
>> -- Bert
>>
>> 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, Jul 13, 2017 at 10:15 AM, David Winsemius
>> <dwinsem...@comcast.net> wrote:
>>>
>>>> On Jul 12, 2017, at 6:58 PM, Ng, Kelvin Sai-cheong <ks...@connect.hku.hk>
>>>> wrote:
>>>>
>>>> Dear all,
>>>>
>>>> I am using the pls package of R to perform partial least square on a set of
>>>> multivariate data. Instead of fitting a linear model, I want to fit my
>>>> data with a quadratic function with interaction terms. But I am not sure
>>>> how. I will use an example to illustrate my problem:
>>>>
>>>> Following the example in the PLS manual:
>>>> ## Read data
>>>> data(gasoline)
>>>> gasTrain <- gasoline[1:50,]
>>>> ## Perform PLS
>>>> gas1 <- plsr(octane ~ NIR, ncomp = 10, data = gasTrain, validation = "LOO")
>>>>
>>>> where octane ~ NIR is the model that this example is fitting with.
>>>>
>>>> NIR is a collective of variables, i.e. NIR spectra consists of 401 diffuse
>>>> reflectance measurements from 900 to 1700 nm.
>>>>
>>>> Instead of fitting with predict.octane[i] = a[0] * NIR[0,i] + a[1] *
>>>> NIR[1,i] + ...
>>>> I want to fit the data with:
>>>> predict.octane[i] = a[0] * NIR[0,i] + a[1] * NIR[1,i] + ... +
>>>> b[0]*NIR[0,i]*NIR[0,i] + b[1] * NIR[0,i]*NIR[1,i] + ...
>>>>
>>>> i.e. quadratic with interaction terms.
>>>>
>>>> But I don't know how to formulate this.
>>>
>>> I did not see any terms in the model that I would have called interaction
>>> terms. I'm seeing a desire for a polynomial function in NIR. For that
>>> purpose, one might see if you get satisfactory results with:
>>>
>>> gas1 <- plsr(octane ~NIR + I(NIR^2), ncomp = 10, data = gasTrain,
>>> validation = "LOO")
>>> gas1
>>>
>>> I first tried using poly(NIR, 2) on the RHS and it threw an error, which
>>> raises concerns in my mind that this may not be a proper model. I have no
>>> experience with the use of plsr or its underlying theory, so the fact that
>>> this is not throwing an error is no guarantee of validity. Using this
>>> construction in ordinary least squares regression has dangers with
>>> inferential statistics because of the correlation of the linear and squared
>>> terms as well as likely violation of homoscedasticity.
>>>
>>> --
>>> David.
>>>
>>>
>>>>
>>>> May I have some help please?
>>>>
>>>> Thanks,
>>>>
>>>> Kelvin
>>>>
>>>> [[alternative HTML version deleted]]
>>>>
>>>> ______________________________________________
>>>> R-help@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.
>>>
>>> David Winsemius
>>> Alameda, CA, USA
>>>
>>> ______________________________________________
>>> R-help@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.
>>
>> ______________________________________________
>> R-help@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.
>
______________________________________________
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