[R] Bug in by() function which works for some FUN argument and does not work for others

Duncan Murdoch murdoch.duncan at gmail.com
Fri Apr 15 11:30:15 CEST 2016


On 15/04/2016 4:16 AM, Akhilesh Singh 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:

See their errata page http://personal.bgsu.edu/~mrizzo/Rx/Rx-errata.txt. 
  They corrected "mean" to "colMeans".

Duncan Murdoch

>
>> 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$Gender: Male
> FSIQ  VIQ    PIQ       Weight    Height   MRI_Count
> 115.00000 115.25000 111.60000 166.44444 71.43158 954855.40000
>
>
> I do not know how could the writers of the book have produced the above
> results by by() function. But, when I could not reproduce these results,
> then I thought that probably, this could possibly be due to some missing
> values NA's in Weight and Height variables. Then I tried the above code for
> the "mtcars" dataset for INDICES=mtcars$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.
>



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