[R] Linear Discriminant Analysis in R
Liaw, Andy
andy_liaw at merck.com
Fri May 28 15:07:19 CEST 2010
cobler_squad needs more basic help than doing lda. The data input just
doesn't make sense.
If vowel_feature is a data frame, than G <- vowel_feature[15] creates
another data frame containing the 15th variable in vowel_feature, so "G"
is the name of a data frame, not a variable in a data frame. The lda()
call makes even less sense. I wonder if he had tried to go through the
examples in the help file and try to understand how it is used?
Andy
> -----Original Message-----
> From: r-help-bounces at r-project.org
> [mailto:r-help-bounces at r-project.org] On Behalf Of Joris Meys
> Sent: Friday, May 28, 2010 8:50 AM
> To: cobbler_squad
> Cc: r-help at r-project.org
> Subject: Re: [R] Linear Discriminant Analysis in R
>
> Could you provide us with data to test the code? use dput
> (and limit the
> size!!!!!)
>
> eg:
> dput(vowel_features)
> dput(mask_features)
>
> Without this information, it's impossible to say what's going
> wrong. It looks like you're doing something wrong in the
> selection. What should vowel_features[15] return? Did you
> check it's actually what you want? Did you use str(G) to
> check the type?
>
> Cheers
> Joris
>
> On Thu, May 27, 2010 at 5:28 PM, cobbler_squad
> <la.foma at gmail.com> wrote:
>
> >
> > Joris,
> >
> > You are a life saver. Based on two sample files above, I think lda
> > should go something like this:
> >
> > vowel_features <- read.table(file = "mappings_for_vowels.txt")
> > mask_features <- data.frame(as.matrix(read.table(file =
> > "3dmaskdump_ICA_37_Combined.txt")))
> > G <- vowel_features[15]
> >
> > cvc_lda <- lda(G~ vowel_features[15], data=mask_features,
> > na.action="na.omit", CV=TRUE)
> >
> > ERROR: Error in model.frame.default(formula = G ~
> vowel_features[15],
> > data = mask_features, :
> > invalid type (list) for variable 'G'
> >
> > I am clearly doing something wrong declaring G (how should
> I declare
> > grouping in R when I need to use one column from
> vowel_feature file)?
> > Sorry for stupid questions and thank you for being so helpful!
> >
> > ---------
> > again, sample files that I am working with:
> >
> > mappings_for_vowels.txt:
> >
> > V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 V11 V12 V13 V14 V15 V16
> V17 V18 V19
> > V20
> > V21 V22 V23 V24 V25 V26
> > 1 E 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0
> 0 0 1 0
> > 0 0 0 0 0 0
> > 2 o 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
> 1 0 1 0
> > 1 0 1 0 0 0
> > 3 I 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0
> 0 1 0 0
> > 0 0 0 0 0 0
> > 4 ^ 0 0 0 0 0 0 0 0 0 0 0 0 1 0 1
> 0 0 1 0
> > 0 0 0 0 0 0
> > 5 @ 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
> 1 0 0 1
> > 0 0 0 0 0 0
> >
> > and the mask_features file is:
> >
> > V42 V43 V44 V45 V46
> > V47 V48 V49
> > [1,] 2.890891625 2.881188521 2.887784444 -2.882606612
> -2.888877341
> > 2.879834384 2.886483229 2.883815864
> > [2,] 2.763404707 2.756198683 2.761863881 -2.756827983
> -2.762268531
> > 2.754305072 2.760017050 2.758399799
> > [3,] 0.556614506 0.556377530 0.556247414 -0.556300910
> -0.556098321
> > 0.557495060 0.557383073 0.556867424 [4,] 0.367065248
> 0.366962036
> > 0.366870087 -0.366794442 -0.366644148
> > 0.366613343 0.366537320 0.366953464
> > [5,] 0.423692393 0.421835623 0.421741829 -0.421897460
> -0.421659824
> > 0.421567705 0.421465738 0.422407838
> >
> > --
> > View this message in context:
> >
> http://r.789695.n4.nabble.com/Linear-Discriminant-Analysis-in-R-tp2231
> > 922p2233333.html Sent from the R help mailing list archive at
> > Nabble.com.
> >
> > ______________________________________________
> > R-help at r-project.org mailing list
> > 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.
> >
>
>
>
> --
> Joris Meys
> Statistical Consultant
>
> Ghent University
> Faculty of Bioscience Engineering
> Department of Applied mathematics, biometrics and process control
>
> Coupure Links 653
> B-9000 Gent
>
> tel : +32 9 264 59 87
> Joris.Meys at Ugent.be
> -------------------------------
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>
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> ______________________________________________
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> 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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