[R-sig-ME] [R] glmutli package assistance please - error Solved
Bill Poling
Bill@Poling @ending from zeli@@com
Thu Nov 15 21:01:11 CET 2018
Hello Michael and all.
1. I replaced INT with Numeric that did not solve the error problem.
2. However I discovered that my matrix was the problem, I had it set to 2,5 and when I set it to 6,6 I no longer get the error, which was due to not having the correct or more than necessary fields in the matrix.
Clues came from: https://stackoverflow.com/questions/15031338/subscript-out-of-bounds-general-definition-and-solution
Following the author's pattern they described their data as needing matrix = 6,6 due to 6 factors and 6 covariates .
I set my matrix to the number of Factors and Covariates, 2-5 and that caused the error.
[,1] [,2]
[1,] 497664 10368
[2,] NA NA
[3,] NA NA
[4,] NA NA
[5,] NA NA
dd <- matrix(nc = 6, nr = 6) View(dd)
for(i in 1:2) for(j in 1:5) dd[i, j] <- glmulti(names(r1a)[1], names(r1a)[c(2:(1 + i), 8:(3 + j))], data = r1a, method = "d")
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 497664 10368 432 36 6 NA
[2,] 16000000 200000 5000 250 25 NA
[3,] NA NA NA NA NA NA
[4,] NA NA NA NA NA NA
[5,] NA NA NA NA NA NA
[6,] NA NA NA NA NA NA
Thank you for your support!
WHP
From: Michael Dewey <lists using dewey.myzen.co.uk>
Sent: Thursday, November 15, 2018 7:24 AM
To: Bill Poling <Bill.Poling using zelis.com>; r-sig-mixed-models using r-project.org; r-help (r-help using r-project.org) <r-help using r-project.org>
Subject: Re: [R] glmutli package assistance please
Dear Bill
I am not sure what is going on here but I notice that 2 of your
covariates are numeric and 3 integer. What happens if you make them all
numeric?
Michael
On 15/11/2018 11:46, Bill Poling wrote:
> Hi, I have removed the pdf which was causing my e-mail to be blocked by moderators, my apologies.
>
> https://www.jstatsoft.org/article/view/v034i12/v34i12.pdf
>
> Original post:
>
> Hello. I am still trying to get some of the examples in this glmulti pdf to work with my data.
>
> I have sent e-mails to author addresses provided but no response or bounced back as in valid.
>
> I am not sure if this is more likely to receive support on r-help or r-sig-mixed-models, hence the double posting, my apologies in advance.
>
> I am windows 10 -- R3.5.1 -- RStudio Version 1.1.456
>
> glmulti: An R Package for Easy Automated Model Selection with (Generalized) Linear Models
>
> pdf Attached:
>
> On page 13 section 3.1 of the pdf they describe a routine to estimate the candidate models possible.
>
> Their data description:
> The number of levels factors have does not affect the number of candidate models, only their complexity. We use a data frame dod, containing as a first column a dummy response variable, the next 6 columns are dummy factors with three levels, and the last six are dummy covariates.
> To compute the number of candidate models when there are between 1 and 6 factors and 1 and 6 covariates, we call glmulti with method = "d" and data = dod. We use names(dod) to specify the names of the response variable and of the predictors. We vary the number of factors and covariates, this way:
>
>
> Their routine:
> dd <- matrix(nc = 6, nr = 6) for(i in 1:6) for(j in 1:6) dd[i, j] <- glmulti(names(dod)[1],
> + names(dod)[c(2:(1 + i), 8:(7 + j))], data = dod, method = "d")
>
> My data, I organized it similar to the example, Response, Factor, Factor, 5 covariates
>
> Classes 'data.table' and 'data.frame':23141 obs. of 8 variables:
> $ Editnumber2 : num 0 0 1 1 1 1 1 1 1 1 ...
> $ PatientGender : Factor w/ 3 levels "F","M","U": 1 1 2 2 2 2 1 1 1 1 ...
> $ B1 : Factor w/ 14 levels "Z","A","C","D",..: 2 2 3 3 2 2 2 2 2 2 ...
> $ SavingsReversed: num -0.139 -0.139 -0.139 -0.139 -0.139 ...
> $ productID : int 3 3 3 3 3 3 3 3 1 1 ...
> $ ProviderID : int 113676 113676 113964 113964 114278 114278 114278 114278 114278 114278 ...
> $ ModCnt : int 0 0 0 0 1 1 1 1 1 1 ...
> $ B2 : num -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 ...
> - attr(*, ".internal.selfref")=<externalptr>
>
> Trying to follow what they did, my routine, Editnumber2 is the response variable:
>
> dd <- matrix(nc = 2, nr = 5)
> for(i in 1:2) for(j in 1:5) dd[i, j] <- glmulti(names(r1)[1], names(r1)[c(2:(1 + i), 7:(6 + j))], data = r1, method = "d")
>
> The error: Error in terms.formula(formula, data = data) :
> invalid model formula in ExtractVars
>
> I have tried changing the numbers around but get results like this:
>
> Initialization...
> TASK: Diagnostic of candidate set.
> Sample size: 23141
> 2 factor(s).
> 2 covariate(s). <--appears to be missing 3 of the covariates for some reason?
> 0 f exclusion(s).
> 0 c exclusion(s).
> 0 f:f exclusion(s).
> 0 c:c exclusion(s).
> 0 f:c exclusion(s).
> Size constraints: min = 0 max = -1
> Complexity constraints: min = 0 max = -1 Your candidate set contains 250 models.
> Error in `[<-`(`*tmp*`, i, j, value = glmulti(names(r1)[1], names(r1)[c(2:(1 + :
> subscript out of bounds
>
>
> I hope someone can help straighten out my code, thank you.
>
>
> WHP
>
>
>
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--
Michael
http://www.dewey.myzen.co.uk/home.html
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