[R] Bug in by() function which works for some FUN argument and does not work for others
Akhilesh Singh
akhileshsingh.igkv at gmail.com
Sun Apr 17 17:11:26 CEST 2016
Dear All,
Yes, I certainly now agree with the suggestion of Adrian Dusa for using
colMeans in place of mean in the situation that I had reported to r-help.
And I am sorry that I did not personally extend my thanks to him. I really
wish to thank him for his suggestion, and I do this now.
However, I wished for future a way to apply a more complex function than
mean, say, e.g. a function for skewness or kurtosis and the likes in the
by() function. The function colMeans would be applicable for mean only.
That is why, I later came to above solution.
Yet, during all these deliberations, I wish to mention the suggestion given
by Dr. Jim Lemon, who suggested to use following code mixing by() into
sapply() wonderfully taking advantage of positional interpretations of
arguments in any R-code, that actually met my objective nicely for my
future project of using more complex functions in lieu of mean:
sapply(brain[,-1],by,brain$Gender,mean,na.rm=TRUE)
FSIQ VIQ PIQ Weight Height MRI_Count
Female 111.9 109.45 110.45 137.2000 65.76500 862654.6
Male 115.0 115.25 111.60 166.4444 71.43158 954855.4
Secondly, I also wish to express my sorry to have mentioned "bug" for the
by() function, instead of thinking that I could be my mistake, whereas I
should have plainly sought help from r-help instead of calling it a "bug".
Had this hurt anybody's feeling, I express my regret and offer my apologies
to all of them for calling this name.
With best regards,
Dr. A.K. Singh
Head, Department of Agril. Statistics
Indira Gandhi Krishi Vishwavidyalaya, Raipur
Chhattisgarh, India, PIN-492012
Mobile: +919752620740
Email: akhileshsingh.igkv at gmail.com
On Sun, Apr 17, 2016 at 7:52 AM, David Winsemius <dwinsemius at comcast.net>
wrote:
>
> > On Apr 16, 2016, at 2:03 AM, Akhilesh Singh <
> akhileshsingh.igkv at gmail.com> wrote:
> >
> > Dear All,
> >
> > I have got your core message, that it is my responsibility to determine
> whether any particular function in my version of R satisfies the language
> requirements at the time of your use. Jim Albert and Maria Rizzo must have
> used their code, which was permitted in the R-code of their time (2012).
> >
> > Therefore, I have now modified my R-code, as per R-3..2.4 version,
> according to my requirement as follows, which is working for my 'brain'
> data set, whose output is reproduced below for your information please:
> >
> > > by(brain[,-1], INDICES=list(Gender=brain$Gender), FUN=function(x,
> na.rm=FALSE) sapply(x, mean, na.rm=na.rm), na.rm=TRUE)
> > Gender: Female
> > FSIQ VIQ PIQ Weight Height MRI_Count
> > 111.900 109.450 110.450 137.200 65.765 862654.600
> >
> --------------------------------------------------------------------------------------------------
> > Gender: Male
> > FSIQ VIQ PIQ Weight Height
> MRI_Count
> > 115.00000 115.25000 111.60000 166.44444 71.43158
> 954855.40000
>
> Yes. that is certainly a workable alternative, although I thought the
> question of "how to to it" had been effectively answered with the
> suggestion from Adrian Dusa to use colMeans. It, too, has an `na.rm=TRUE`
> option
>
> I was only responding to your plaintive complaint that the current version
> of R had a "bug" because it was not behaving as promised by an introductory
> text with a three year-old publishing date.
>
> --
> David.
>
>
> >
> > With best regards,
> >
> > Dr. A.K. Singh
> > Head, Department of Agril. Statistics
> > Indira Gandhi Krishi Vishwavidyalaya, Raipur
> > Chhattisgarh, India, PIN-492012
> > Mobile: +919752620740
> > Email: akhileshsingh.igkv at gmail.com
> >
> > On Fri, Apr 15, 2016 at 2:24 PM, David Winsemius <dwinsemius at comcast.net>
> wrote:
> >
> > > On Apr 15, 2016, at 1:16 AM, Akhilesh Singh <
> akhileshsingh.igkv at gmail.com> wrote:
> > >
> > > Dear All,
> > >
> > > Thanks for your help. However, I would like to draw your attention to
> the
> > > following:
> > >
> > > Actually, I was replicating the Example 2.3, using the dataset
> > > "brainsize.txt" given in Section 2.3.3 ("Summarize by group") at page
> 55,
> > > of a famous book "R by Example" written by "Jim Albert and Maria Rizzo"
> > > published in Springers (2012) in a Use R! Series. The output of the
> by()
> > > function printed in the book is being reproduced below for information
> to
> > > all:
> > >
> > >> by(data=brain[, -1], INDICES=brain$Gender, FUN=mean, na.rm=TRUE)
> > > brain$Gender: Female
> > > FSIQ VIQ PIQ Weight Height MRI_Count
> > > 111.900 109.450 110.450 137.200 65.765 862654.600
> > > ------------------------------------------------------------
> > > brain$Gender: Male
> > > FSIQ VIQ PIQ Weight Height MRI_Count
> > > 115.00000 115.25000 111.60000 166.44444 71.43158 954855.40000
> > >
> > >
> > > I do not know how could the writers of the book have produced the above
> > > results by by() function.
> >
> >
> > There was in the not-so-distant past a function named `mean.data.frame`
> which would have "worked" in that instance. That function was removed. I
> thought you could find the exact date of that action by searching the NEWS
> but failed. Reviewing the citations of `mean.data.frame` in the r-help
> archives I see that users were being warned that its use was deprecated in
> mid 2012. It's very possible that the authors of a book in 2012 were using
> an earlier version of R that had that facility available to them before it
> was deprecated. With a more than current version of R 3.3.0 and a modest
> number of loaded packages I see this:
> >
> > > methods(mean)
> > [1] mean,ANY-method mean,Matrix-method mean,Raster-method
> > [4] mean,sparseMatrix-method mean,sparseVector-method mean.Date
> > [7] mean.default mean.difftime mean.POSIXct
> > [10] mean.POSIXlt mean.yearmon* mean.yearqtr*
> > [13] mean.zoo*
> >
> > It is your responsibility to determine whether any particular function
> in your version of R satisfies the language requirements at the time of
> your use. Jim Albert and Maria Rizzo do not set the standards for what is
> an evolving piece of software.
> >
> > --
> > David.
> >
> >
> > > But, when I could not reproduce these results,
> > > then I thought that probably, this could possibly be due to some
> missing
> > > values NA's in Weight and Height variables. Then I tried the above
> code for
> > > the "mtcars" dataset for INDICES=mtcars$am. When I found the same
> results
> > > here too, then I reported the case in "r-help at R-project.org".
> > >
> > > With best regards,
> > >
> > > Dr. A.K. Singh
> > > Head, Department of Agril. Statistics
> > > Indira Gandhi Krishi Vishwavidyalaya, Raipur
> > > Chhattisgarh, India, PIN-492012
> > > Mobile: +919752620740
> > > Email: akhileshsingh.igkv at gmail.com
> > >
> > > On Fri, Apr 15, 2016 at 3:06 AM, Adrian Dușa <dusa.adrian at unibuc.ro>
> wrote:
> > >
> > >> I think you are not using the best function for what your intentions
> are.
> > >> Try:
> > >>
> > >>> by(data=mtcars, INDICES=list(as.factor(mtcars$am)), FUN=colMeans)
> > >> : 0
> > >> mpg cyl disp hp drat wt
> > >> qsec vs
> > >> 17.1473684 6.9473684 290.3789474 160.2631579 3.2863158 3.7688947
> > >> 18.1831579 0.3684211
> > >> am gear carb
> > >> 0.0000000 3.2105263 2.7368421
> > >>
> > >>
> ---------------------------------------------------------------------------
> > >> : 1
> > >> mpg cyl disp hp drat wt
> > >> qsec vs
> > >> 24.3923077 5.0769231 143.5307692 126.8461538 4.0500000 2.4110000
> > >> 17.3600000 0.5384615
> > >> am gear carb
> > >> 1.0000000 4.3846154 2.9230769
> > >>
> > >> See the difference between colMeans() and mean() in their respective
> help
> > >> files.
> > >> Hth,
> > >> Adrian
> > >>
> > >> On Thu, Apr 14, 2016 at 11:14 PM, Akhilesh Singh <
> > >> akhileshsingh.igkv at gmail.com> wrote:
> > >>
> > >>> Dear Sirs,
> > >>>
> > >>> I am Professor at Indira Gandhi Krishi Vishwavidyalaya, Raipur,
> > >>> Chhattisgarh, India.
> > >>>
> > >>> While taking classes, I found the *by() *function producing following
> > >>> error
> > >>>
> > >>> when I use FUN=mean or median and some other functions, however,
> > >>> FUN=summary works.
> > >>>
> > >>> Given below is the output of the example I used on a built-in dataset
> > >>> "mtcars", along with error message reproduced herewith:
> > >>>
> > >>>> by(data=mtcars, INDICES=list(mtcars$am), FUN=mean)
> > >>> : 0
> > >>> [1] NA
> > >>> ------------------------------------------------------------
> > >>> : 1
> > >>> [1] NA
> > >>> Warning messages:
> > >>> 1: In mean.default(data[x, , drop = FALSE], ...) :
> > >>> argument is not numeric or logical: returning NA
> > >>> 2: In mean.default(data[x, , drop = FALSE], ...) :
> > >>> argument is not numeric or logical: returning NA
> > >>>
> > >>> However, the same by() function works for FUN=summary, given below
> is the
> > >>> output:
> > >>>
> > >>>> by(data=mtcars, INDICES=list(mtcars$am), FUN=summary)
> > >>> : 0
> > >>> mpg cyl disp hp
> > >>> Min. :10.40 Min. :4.000 Min. :120.1 Min. : 62.0
> > >>> 1st Qu.:14.95 1st Qu.:6.000 1st Qu.:196.3 1st Qu.:116.5
> > >>> Median :17.30 Median :8.000 Median :275.8 Median :175.0
> > >>> Mean :17.15 Mean :6.947 Mean :290.4 Mean :160.3
> > >>> 3rd Qu.:19.20 3rd Qu.:8.000 3rd Qu.:360.0 3rd Qu.:192.5
> > >>> Max. :24.40 Max. :8.000 Max. :472.0 Max. :245.0
> > >>> drat wt qsec vs
> am
> > >>>
> > >>> Min. :2.760 Min. :2.465 Min. :15.41 Min. :0.0000 Min.
> > >>> :0
> > >>>
> > >>> 1st Qu.:3.070 1st Qu.:3.438 1st Qu.:17.18 1st Qu.:0.0000 1st
> > >>> Qu.:0
> > >>>
> > >>> Median :3.150 Median :3.520 Median :17.82 Median :0.0000
> Median
> > >>> :0
> > >>>
> > >>> Mean :3.286 Mean :3.769 Mean :18.18 Mean :0.3684 Mean
> > >>> :0
> > >>>
> > >>> 3rd Qu.:3.695 3rd Qu.:3.842 3rd Qu.:19.17 3rd Qu.:1.0000 3rd
> > >>> Qu.:0
> > >>>
> > >>> Max. :3.920 Max. :5.424 Max. :22.90 Max. :1.0000 Max.
> > >>> :0
> > >>>
> > >>> gear carb
> > >>> Min. :3.000 Min. :1.000
> > >>> 1st Qu.:3.000 1st Qu.:2.000
> > >>> Median :3.000 Median :3.000
> > >>> Mean :3.211 Mean :2.737
> > >>> 3rd Qu.:3.000 3rd Qu.:4.000
> > >>> Max. :4.000 Max. :4.000
> > >>> ------------------------------------------------------------
> > >>> : 1
> > >>> mpg cyl disp hp
> drat
> > >>>
> > >>> Min. :15.00 Min. :4.000 Min. : 71.1 Min. : 52.0 Min.
> > >>> :3.54
> > >>> 1st Qu.:21.00 1st Qu.:4.000 1st Qu.: 79.0 1st Qu.: 66.0 1st
> > >>> Qu.:3.85
> > >>> Median :22.80 Median :4.000 Median :120.3 Median :109.0
> Median
> > >>> :4.08
> > >>> Mean :24.39 Mean :5.077 Mean :143.5 Mean :126.8 Mean
> > >>> :4.05
> > >>> 3rd Qu.:30.40 3rd Qu.:6.000 3rd Qu.:160.0 3rd Qu.:113.0 3rd
> > >>> Qu.:4.22
> > >>> Max. :33.90 Max. :8.000 Max. :351.0 Max. :335.0 Max.
> > >>> :4.93
> > >>> wt qsec vs am
> gear
> > >>>
> > >>> Min. :1.513 Min. :14.50 Min. :0.0000 Min. :1 Min.
> > >>> :4.000
> > >>>
> > >>> 1st Qu.:1.935 1st Qu.:16.46 1st Qu.:0.0000 1st Qu.:1 1st
> > >>> Qu.:4.000
> > >>>
> > >>> Median :2.320 Median :17.02 Median :1.0000 Median :1 Median
> > >>> :4.000
> > >>>
> > >>> Mean :2.411 Mean :17.36 Mean :0.5385 Mean :1 Mean
> > >>> :4.385
> > >>>
> > >>> 3rd Qu.:2.780 3rd Qu.:18.61 3rd Qu.:1.0000 3rd Qu.:1 3rd
> > >>> Qu.:5.000
> > >>>
> > >>> Max. :3.570 Max. :19.90 Max. :1.0000 Max. :1 Max.
> > >>> :5.000
> > >>>
> > >>> carb
> > >>> Min. :1.000
> > >>> 1st Qu.:1.000
> > >>> Median :2.000
> > >>> Mean :2.923
> > >>> 3rd Qu.:4.000
> > >>> Max. :8.000
> > >>>>
> > >>>
> > >>> I am using the latest version of *R-3.2.4 on Windows*, however, this
> error
> > >>> is being generated in the previous version too,
> > >>>
> > >>> Hope this reporting will get serious attention in debugging.
> > >>>
> > >>> With best regards,
> > >>>
> > >>> Dr. A.K. Singh
> > >>> Head, Department of Agril. Statistics
> > >>> Indira Gandhi Krishi Vishwavidyalaya, Raipur
> > >>> Chhattisgarh, India, PIN-492012
> > >>> Mobile: +919752620740
> > >>> Email: akhileshsingh.igkv at gmail.com
> > >>>
> > >>> [[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.
> > >>>
> > >>
> > >>
> > >>
> > >> --
> > >> Adrian Dusa
> > >> University of Bucharest
> > >> Romanian Social Data Archive
> > >> Soseaua Panduri nr.90
> > >> 050663 Bucharest sector 5
> > >> Romania
> > >>
> > >
> > > [[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.
> >
> > David Winsemius
> > Alameda, CA, USA
> >
> >
>
> David Winsemius
> Alameda, CA, USA
>
>
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