[R] Bug in by() function which works for some FUN argument and does not work for others
Akhilesh Singh
akhileshsingh.igkv at gmail.com
Sat Apr 16 11:03:04 CEST 2016
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$Gender), FUN=function(x,
na.rm=FALSE) sapply(x, mean, na.rm=na.rm), na.rm=TRUE)
Gender: Female
FSIQ VIQ PIQ Weight Height MRI_Count
111.900 109.450 110.450 137.200 65.765 862654.600
--------------------------------------------------------------------------------------------------
Gender: Male
FSIQ VIQ PIQ Weight Height
MRI_Count
115.00000 115.25000 111.60000 166.44444 71.43158
954855.40000
With best regards,
Dr. A.K. Singh
Head, Department of Agril. Statistics
Indira Gandhi Krishi Vishwavidyalaya, Raipur
Chhattisgarh, India, PIN-492012
Mobile: +919752620740
Email: akhileshsingh.igkv at gmail.com
On Fri, Apr 15, 2016 at 2:24 PM, David Winsemius <dwinsemius at comcast.net>
wrote:
>
> > On Apr 15, 2016, at 1:16 AM, Akhilesh Singh <
> akhileshsingh.igkv at gmail.com> wrote:
> >
> > Dear All,
> >
> > Thanks for your help. However, I would like to draw your attention to the
> > following:
> >
> > Actually, I was replicating the Example 2.3, using the dataset
> > "brainsize.txt" given in Section 2.3.3 ("Summarize by group") at page 55,
> > of a famous book "R by Example" written by "Jim Albert and Maria Rizzo"
> > published in Springers (2012) in a Use R! Series. The output of the by()
> > function printed in the book is being reproduced below for information to
> > all:
> >
> >> by(data=brain[, -1], INDICES=brain$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
>
>
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